commit 6e38beb62839e566480cd3fd9a1e63eff46e7f2e
Merge: 6da32a4 b7cc2b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Mar 5 13:19:45 2017 -0500

    Merge pull request #26 from atmyers/development
    
    Capture the return code of analysis scripts in the test suite

commit b7cc2b393b8d8f814f21e3bc888e4caea007507b
Author: Andrew Myers <atmyers2@gmail.com>
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 a43f9c4b8deb3adf4a2224bb3cce25a1a43ef94c
Merge: f370653 6da32a4
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 15:47:15 2017 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development
    
    merging.

commit f370653d2cc074277ba611b1cca3e932badc957e
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Fri Mar 3 15:44:39 2017 -0800

    Add my computer name to the list of CCSE_machines

Tools/C_mk/Make.machines

commit 6da32a472f59314038e6069bc13f2ec659812752
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 28 10:20:45 2017 -0500

    address the case where no benchmark is found (we now say so on the report page)
    and also plot variables that start with "diff"

Tools/RegressionTesting/test_report.py

commit 810b21be280664ff6d390a3f2d7d7cdd3edfe22a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 10 11:12:40 2017 -0800

    add a new tilebox function

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit f4d4dcdb6bf6bee31acfedf34397087b6305df4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 7 09:09:43 2017 -0800

    fix extra argument

Src/C_BaseLib/BaseFab_nd.f90

commit 6967225541d7f8133e0e19c359ec74925ac29408
Merge: d8e93a8 437079c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 11:34:09 2017 -0800

    Merge branch 'master' into development

commit 437079cd36e59dda20f0d0f80fa3bc5dc0b8b10d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 11:33:51 2017 -0800

    fix a bug in tutorial

Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit d8e93a8fab5fc2d03c97529e1b21d0285674d356
Merge: 702313a 20217b7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 3 15:58:50 2017 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 20217b76506bebd185c1dabeea1a6fe24f25d1c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 3 08:36:54 2017 -0800

    fix a tutorial

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 98ba3620aec842b938b526498d159fd5de2cbe33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a226064ba602027d0272343fb2c9b9464624ae9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 29 11:59:11 2017 -0500

    allow for multiple selected variables to be chosen via the -v flag,
    as a single string with names space-separated

Tools/Postprocessing/F_Src/fextract.f90

commit a3118bfceac8560c2b148b5dda55540ece1f2c43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 27 10:49:01 2017 -0500

    add % of domain covered

Tools/Postprocessing/F_Src/fboxinfo.f90

commit 702313af3b6d6ddec9a63547971db9f0fbc5ad97
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Jan 25 13:29:42 2017 -0800

    fix utility

Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp

commit b65ccdc7c2905b116ca035ee207ad05a438f68c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 038088debcc084e6897b16a3dab8cf0447cd53bf
Merge: 6b696e4 1208914
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Tue Jan 24 16:33:14 2017 -0800

    Merge pull request #25 from atmyers/development
    
    Changes needed to use the regression test suite with WarpX's python mode

commit 120891496b587b6ef4192a44d629b25acf4d8b70
Author: Andrew Myers <atmyers2@gmail.com>
Date:   Tue Jan 24 15:31:10 2017 -0800

    Changes needed to use the regression test suite with WarpX's python mode.

Tools/RegressionTesting/regtest.py
Tools/RegressionTesting/suite.py

commit 6b696e4b38e4896fe91f6678c161315fc6b4e837
Merge: 4814bcc 4c3ba82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 15:37:36 2017 -0800

    Merge branch 'master' into development

commit 4814bcc783a9a415a6a1516289e2cb050130c860
Merge: 12fe9c1 6e53518
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Jan 13 15:36:00 2017 -0800

    Merge pull request #24 from zingale/development
    
    switch from git tag to describe

commit 6e535187ef1a260c6c50e5047d99fdf9e0f300d0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 13 18:01:53 2017 -0500

    add --dirty

Tools/C_scripts/makebuildinfo_C.py

commit deb9033e22f0568d8e332ab62504c20381f938d0
Merge: 69a6d21 9d549f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 13 17:54:44 2017 -0500

    Merge branch 'development' of ssh://github.com/zingale/BoxLib into development

commit 69a6d21c9deeb544651165c45181f1cbe69b2f15
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 13 17:54:13 2017 -0500

    switch from a hash to describe

Tools/C_scripts/makebuildinfo_C.py

commit 4c3ba82e793a6b9663ff4a064b3ab46410f7f243
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 34dc15493dc0d078bd14e7793f8dccce92306836
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 4 12:50:39 2017 -0800

    remove unsafe assertions

Src/C_BaseLib/BoxArray.cpp

commit c114717e6c47188a0812804addcab61d7605ef89
Merge: 01285b0 57f5bf7
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jan 4 08:49:22 2017 -0800

    Merge pull request #23 from mathstuf/pic-option
    
    cmake: add an option for compiling with -fPIC

commit 01285b0051754e5a719fa2a3872a682c79d57d5f
Merge: 44b39fd 043954c
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Wed Jan 4 08:48:28 2017 -0800

    Merge pull request #22 from mathstuf/cmake-flag-manipulation
    
    CCSEOptions: construct flags properly

commit 57f5bf74476617302659219d82e465e4759a1293
Author: Ben Boeckel <ben.boeckel@kitware.com>
Date:   Wed Jan 4 10:46:24 2017 -0500

    cmake: add an option for compiling with -fPIC
    
    This is required to support linking the library from an executable which
    uses other shared libraries.

CMakeLists.txt
Tools/CMake/CCSEOptions.cmake

commit 043954ce6d017f16833f8b4018d0eb9914a332dc
Author: Ben Boeckel <ben.boeckel@kitware.com>
Date:   Wed Jan 4 10:46:01 2017 -0500

    CCSEOptions: construct flags properly
    
    The `CMAKE_<LANG>_FLAGS` variables are strings, not lists, so
    `list(APPEND)` should not be used.

Tools/CMake/CCSEOptions.cmake

commit 44b39fd5384cd15a2d0ff568199c0cfcbc75666a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 3 10:05:58 2017 -0800

    some unsigned to int conversion for OPAL

Src/C_BaseLib/FabArray.H
Src/C_ParticleLib/Particles.H

commit 3601a9e9a544aa0c25c825d44bdc6c6512122cbf
Merge: 12fe9c1 9d549f5
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
Date:   Fri Dec 30 12:59:55 2016 -0800

    Merge pull request #21 from zingale/development
    
    fix case where no files are found for copying

commit 9d549f5c3b5000f2d6fa50740b9a942760e86aa4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Dec 30 10:23:07 2016 -0500

    fix case where no files are found for copying

Tools/RegressionTesting/regtest.py

commit 12fe9c19a66d0a7b68466f2a8915f3f689ea9f51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 14 08:54:56 2016 -0800

    fix 2d addNParticles

Src/C_ParticleLib/Particles.H

commit 52a33992c9bef954590395ea76f52f98589a591c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 14:24:13 2016 -0800

    Release 16.12.1

ReleaseNotes/release-notes-16.12.1

commit 022f93c6e6cb42b28180116b9adbf7cc4c0835be
Merge: 0edba14 f48a5eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 13:56:06 2016 -0800

    Merge branch 'master' into development

commit 0edba1491d75581366639a96e1b0059ca85c825b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 13 13:27:09 2016 -0800

    fix generic plotfile writer

Src/C_BaseLib/PlotFileUtil.cpp

commit 8254951f730f3b0a2114c39d41f3a826e1258329
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:40:41 2016 -0800

    fix comment, format.

Src/C_BaseLib/PlotFileUtil.H

commit 59ee7fddd494088e6eacc362fe53ceb4bd28da80
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:34:57 2016 -0800

    clarify comment.

Src/C_BaseLib/PlotFileUtil.H

commit 563bb08e36c82876120a89912676277f03650859
Merge: c0f427f 999ee83
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:27:06 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit c0f427ffd1f4f85f46ec5be2c89a1f6822bf14bc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:26:45 2016 -0800

    fix comments, back.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 385daa0ce5a9f7dd32e5e3358e809a806970ea88
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 13 11:25:04 2016 -0800

    call new function to prebuild directories.

Src/C_AMRLib/Amr.cpp

commit 999ee83cb86779aa6ef47f6f33d9200727ccfdd6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f48a5ebdadbd8ca8c755d45106febbadd95de7e8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 12 16:29:21 2016 -0800

    First pass at addNParticles function in ParticleContainer class.

Src/C_ParticleLib/Particles.H

commit e7c40f776470d49950e52affb82d028aa6a78bed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a3aab119670f0ea853b5c5712d7c1766765115e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b138b03388c2c22f453f29b3436b3c625e97e87b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 9 12:04:16 2016 -0800

    remove static.

Src/C_BaseLib/PlotFileUtil.H

commit c29776a65a824fd5a8fe5b00c580fe70aa4539b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 9 10:13:40 2016 -0800

    better way to detect Open MPI

Tools/C_mk/sites/Make.unknown

commit 06deceff62a48ef8906941742f225020cbcbfb18
Author: vince <vebeckner@lbl.gov>
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 f3840d8c41d5cabd35d1e632f0c77d630e3b3498
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 8 16:01:24 2016 -0800

    functions for generic plotfiles.

Src/C_BaseLib/PlotFileUtil.H
Src/C_BaseLib/PlotFileUtil.cpp

commit 117cf7a69eb342bfff17c93ae110d3c59c76497c
Merge: 38bdc6f d21ce8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 38bdc6fd32c9585e112c3f8751027acd989aefa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 96ed1879934d12d92a0d0c21863e379035fed7c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 09ce7a93494b2a9df8c5ed24400024b20fbc1c75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e4a0174d08abcf45071cad32fa6512c364434906
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8db962333edf1c70b9f90fbba2005acc841b257
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 09:02:56 2016 -0800

    Release Notes for BoxLib 16.12

ReleaseNotes/release-notes-16.12

commit a292fe30405e92d2d519ca20fbf36ca9377f5c72
Merge: 68cd920 5981240
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 2 08:35:31 2016 -0800

    Merge branch 'master' into development

commit 68cd920ad003ff87259abd2b47dff0f66665d3d8
Merge: 67b3f9c bf891ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 bf891ba505df61ea901262486206cbc6a9b1f7c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d4a3af4ec49472f546bc917f1cd5029cdf0288fe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 67b3f9c93eaa1f49983a07078518b89429a4e143
Merge: 374357f f430d84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f430d84cb18e4ee61bbe41ff787bb41f6ca6a74b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 1 19:22:12 2016 -0500

    address Weiqun's PR comments

Tools/F_scripts/dep.py

commit f28293e1d4fa2de063e6ce6881cf74979615adfa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 374357f5664efdc4bb5aa1decf6437b76abbf520
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 1 14:09:42 2016 -0800

    make extra stream flushes the default for now.

Src/C_BaseLib/VisMF.cpp

commit 188d63c8b6629fd418fdc7cc2dced2353ee030ad
Merge: 26b290a 918e06d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 1 13:23:17 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 918e06dfc2ce4f5422a950da84d49ce2a2d47d48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 1 12:43:35 2016 -0800

    intel: link with multi-threaded fortran library

Tools/C_mk/comps/intel.mak

commit 3b82103657a52b7fce8ad6ac5d5743a931c92596
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 46debf1b8f938ec79f57b71fdfc24bfe4eb35aa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d21ce8f877d15bac76b47cf832bd5708f3598342
Author: Noah D. Brenowitz <nbren12@gmail.com>
Date:   Wed Nov 30 22:45:55 2016 -0500

    remove bash stuff

Tools/F_scripts/dep.py

commit ee5e5de582f2100207aeb94abb25b937847b0c60
Author: Noah D. Brenowitz <nbren12@gmail.com>
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 52550d6756a28f31ba5b76e8c0281942a1d0bf72
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 30 17:39:38 2016 -0800

    added flush options to try to fix titan.

Src/C_BaseLib/VisMF.cpp

commit 9ffecde6469adf3432ac963db3120db49b795115
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 26b290a33e9229a16259761374302784a9de6551
Merge: bef6d66 90ea36b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 30 14:32:13 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit c9becf134325d35198ee8bcad99cd7df20e64ddf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 14:27:32 2016 -0800

    gcc: trap integer overflow

Tools/C_mk/comps/gnu.mak

commit 90ea36bf9b5d5ba90e4aaeab0c023c5ee8dff803
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3daeda968ed2ec8e66259ff30a91750dae20b6eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6668abfda83e5a9fc6b479aa47e3d2200956d6d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 09:17:17 2016 -0800

    fix make for a test

Tests/C_BaseLib/GNUmakefile

commit a2136c184c7306153163efdb2c4e207e304e7b7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 30 08:55:47 2016 -0800

    fix a dangling pointer

Src/C_BaseLib/FabArray.H

commit 9f1393eac9ad1f47114024e054f8086b0847f650
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bef6d663b803c1da68f717fa1f999436a190b337
Merge: 5959d80 22b9141
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 29 10:43:30 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 22b9141157ff95fabae2e1cfe7e749d8486c5a91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1f5599111aba591eb8f4bba5d1ee3011ba814f6d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 28 14:15:10 2016 -0800

    fix memory leak

Src/C_BaseLib/VisMF.cpp

commit 732162a6ac435972dcf1b9f13229524d2e1bef71
Author: Ann Almgren <asalmgren@lbl.gov>
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 5981240513fcdf4bca3a1db816d484db53560aab
Author: Ann Almgren <asalmgren@lbl.gov>
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 c31024e152461fa66d2f6c5e3ceaef867f268f70
Merge: 70985bb 3f88aba
Author: WeiqunZhang <WeiqunZhang@lbl.gov>
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 3f88aba6671c34a0f0fb426ffc0c3b55c237038a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 28 13:19:15 2016 -0500

    add USE_GPROF to enable profiling with gprof

Tools/C_mk/comps/gnu.mak

commit 70985bbe7fd405313ab47425e7a64f31439eef6a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 365a4e9233cc461781e275dc9be612840e13d216
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 22:42:53 2016 -0500

    isinf --> std::isinf

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit f536a28bdd25f675f2fe333a921a9f9f70fe1b92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7ec47c8cdf55aab36714c12491f6f1fd213a5ad4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 12:32:47 2016 -0800

    Intel: add more checks

Tools/C_mk/comps/intel.mak

commit b5c10a6ea052a760d55261af05f92032e8315726
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 73d19d20d5718792e6e437fb40ca67a4fd310764
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2be838c5a6fd4ed332004c082ccfb839f0af77ca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 26 11:26:39 2016 -0800

    force implicit none for f90 files with gnu

Tools/C_mk/comps/gnu.mak

commit 5959d808b01b4cdc98c155cb4e1409b5fe0d7f40
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 23 11:42:50 2016 -0800

    fix comments.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 7860f851a8e7ed560ebeb898742a11d96f345942
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9b4c4dfc4e19b5cc12b2209820b9f9796c491266
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 12c4332b02c88c2b30f3fa913859010018329567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1adbcda6d278b10239764f7772bf61f72d2592a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 22 11:11:03 2016 -0800

    std::min -> std::min<int> because Array::size() returns size_t now

Src/C_BaseLib/VisMF.cpp

commit 67752f677165e4a42060428fdf6ca9724a86436e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 10:45:54 2016 -0800

    more helpful message

Tools/C_mk/Make.rules

commit 2b28b7be21cf35590d0bd9177a6fdf1ebe63d3bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 17:01:10 2016 -0800

    mpif90 -->

Tools/C_mk/sites/Make.unknown

commit 21fce1be4c8122fde085a096ffcbdb08bc41a501
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 15 16:14:53 2016 -0800

    more intelligent way of adding link flags

Tools/C_mk/sites/Make.unknown

commit 17a22481484c83ea936ff2bbcfb93b70d0508bc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f59972f22b15b2d2d6e07d66e29f46e31def3e63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fc381bbca5cc26694d73c02e55781cdfd69cdef9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b94c1654e8d24bf62d4092e29591d7d643bd80e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 92ffa41ce280312df69f22c4e3d3af7f194beba7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 11 12:29:20 2016 -0800

    fix  in make

Tools/C_mk/Make.defs
Tools/C_mk/Make.rules

commit b2ff35199f5726c47619d7103fe92c4ab6d5c816
Merge: a4f3ea9 3c55e33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a4f3ea913289dec8fa61a0cbf4dc0e1a735982c5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 21 13:24:13 2016 -0800

    fix for ieee_32 rd.

Src/C_BaseLib/VisMF.cpp

commit cd5d9ef48b08e1134487fe27edac67262d7187ae
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 14:54:22 2016 -0800

    clean up debugging diagnostics.

Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.cpp

commit 611d5e3a5eaa3d618bdf297a293b2873daab50bb
Merge: 7995261 19d6098
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 13:00:50 2016 -0800

    merge fix.

commit 799526165e97d110d836d4be5a40e6ba1fe475f1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:57:26 2016 -0800

    output cleanup.

Src/C_BaseLib/VisMF.cpp

commit 5a333bb429fae9b5c697b5f48f01ec99c45bd41f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:56:33 2016 -0800

    additions to i/o documentation.

Docs/Notes.io_implementation
Docs/Readme.io

commit 29d9f74ea67557c99a3d458ebe6d65e47e4ace86
Merge: 87e0c46 9017579
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 18 12:07:28 2016 -0800

    Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio

commit 901757962f9ded2ea9071f1f974abd94339bed38
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 17 16:19:15 2016 -0800

    combine nfiles dependent iterators.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 19d60984bdb3ca8413e39f285585ae61d260ccc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 87e0c463923c71fe46275de803946937ab592ce6
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 16 15:33:02 2016 -0800

    fix comment.

Src/C_BaseLib/NFiles.H

commit 7c7850c798aed5c29a6070636ad0596c4713f77f
Author: Marc Day <MSDay@lbl.gov>
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 1dd1af6e5d25e34f6ec2864a42593fc85abe2806
Merge: 63671d6 e5ac3aa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 16 16:16:52 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 63671d634c2e150c7c4ac5b480c954321191c58d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 16 16:16:37 2016 -0500

    add a heavily commented example inputs file

Tools/RegressionTesting/example-tests.ini

commit e5ac3aac39ceeeb7ce595c4546c4bbc6084be7e9
Merge: 80404fc 0b13262
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 09:18:11 2016 -0800

    Merge branch 'fnodalfillpatch' into development

commit 80404fc3c50deebcc9ff689ae89cbcbf4bfcb9b7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Wed Nov 16 01:25:59 2016 -0500

    Fix error message

Src/C_AMRLib/Amr.cpp

commit 624c49fd48653029553dd65fb1045b36ede25611
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3a7213d120d12d52f73fc82db10b379370137fd9
Merge: 943f030 6deb8e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6deb8e5178a93f7a085b544a71012c9ce59b59e1
Author: Jon Rood <jrood@nrel.gov>
Date:   Tue Nov 15 15:59:44 2016 -0700

    Reducing exception to only OSError.

Tools/RegressionTesting/regtest.py

commit 7c886bdab2a19617c87b8b6bd59486804e614d6b
Author: Jon Rood <jrood@nrel.gov>
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 9b916e36d34ab8d32379a2ade362f2d538b9e127
Author: vince <vebeckner@lbl.gov>
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 94edfe3d6faad2bc9c8422a084d849b207341a3b
Author: vince <vebeckner@lbl.gov>
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 c62adc90568bdd6d6a72eebb605f3560063ab219
Author: vince <vebeckner@lbl.gov>
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 7f1c62a40fcf933bd7c544a417a047afa8668f45
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 13:30:16 2016 -0800

    output for verbose only, remove unused var.

Src/C_AMRLib/Amr.cpp

commit 25e1b087f081097c983f313312b94a329132097e
Author: vince <vebeckner@lbl.gov>
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 c81a9def247b51213c3308340c77f0d7eee81bdc
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 11 12:45:40 2016 -0800

    change function name.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 943f030366fbf85556f9c59765c632ee7ccabbc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5288c043fecd3f9af838b68425b44cd7f10e3997
Merge: 9033929 5ec341b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Nov 9 19:37:30 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 903392928617c740619e8d1d563e1c2d72c1b29e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3c55e33b7ea46c7818e535b4960917735e56b1a8
Merge: 855d3ab 5ec341b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 9 10:27:46 2016 -0800

    Merge branch 'development' into experimental

commit 5ec341bc4945c8a5eb3dccb3bf6e27c8dad1cf4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 855d3ab8e7442e2d4e08d695051e4ee904c59d5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a0fdcb1e4e5a71358d1e0ba13e4a3a53c7fcdc27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 116a3c82f2a5cbd7518b0317d05a617eb010f950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 91139e84109bbdece29329815c9d52e865b7f639
Author: vince <vebeckner@lbl.gov>
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 763d40de7089057e0c4e9efb5b23f10a0ca90b51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6db7238fcbbc09649b178ea5864671d839c843c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0a4289e158faa52745188736907920f36fa457b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 8 13:34:44 2016 -0800

    need to pass fincludes into MODDEP

Tools/C_mk/Make.rules

commit f9fdf39b0b7007925e10fef36d68b7d38845c29d
Merge: a94a542 870356b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a94a542bec013763ef53429fd814d8e0a411a19b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 17:06:03 2016 -0800

    try to detect mpich or openmpi

Tools/C_mk/sites/Make.unknown

commit 8601f2e6f1dc7159344b50562a1a003425c40739
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:37:48 2016 -0800

    more on README.md

Tools/C_mk/README.md

commit 4a9abfd9ecd2fba6b03df9746d5fe7ed9d7c1678
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:25:45 2016 -0800

    minor

Tools/C_mk/README.md

commit 2a953fdca757e1a423f9c9db2785cebd6cfe9d0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 7 16:22:08 2016 -0800

    fix format

Tools/C_mk/README.md

commit cba55c7d8626206345f157265299c36c9dca34da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 870356bbba96593354337350bd8017ae4ce604dd
Author: Brian Friesen <bfriesen@lbl.gov>
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 618b12bc587ef1435d3c0493cc616e31edce1504
Author: Brian Friesen <bfriesen@lbl.gov>
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 5110c59f062ca157a301a808fbcc21a7974bd923
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 22c03f20e3e5ea488e17145bf22d802fc88938e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 6 12:08:51 2016 -0800

    add python to build requirement

Tools/C_mk/README.md

commit 6b1063aa7ba23bcd0e54c3038aff93e38674995d
Merge: 4ebc314 0d1366e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Nov 5 21:40:01 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4ebc314cc8d077b664092ff15534c8fc0eed0d3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 728bf0607159971efe38f2ae0886f24630a0f12d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 960544637190137e7c7c63e68336a26c604abf0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2ffa34a88f41baccc13e9238e13ac71f0aba57b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a8526ded7b7187367808b7042506bd3936f20d4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 17a83d162275f8bc58830c873b4d0c8724a2747e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f37391551d24bf6f3d42fc7704568ee6b364cc53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 13:35:11 2016 -0400

    Make.olcf: link to mpichf90

Tools/C_mk/sites/Make.olcf

commit 7cef502d88ae8e579e51f9cf731fee260277f111
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 4 10:30:11 2016 -0700

    fix missing $ in gnu.mak

Tools/C_mk/comps/gnu.mak

commit 7e309d91448ffa5d3dc810dbca0e1019b64f42e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/gcc.mak
Tools/C_mk/comps/gnu.mak
Tools/C_mk/sites/Make.olcf
Tools/C_mk/sites/Make.unknown

commit ef3c38233f8e604ae5162fda05015c8acbe51a3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 51bfe1b1be1f3d46f469c4c4c9a51820cc3728d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3f6775fafe199b1ecc66e03d989b9637ef15b29a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8e624553b6c81d64b709f3c09e8ab2ab0151965
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c33e6005f6d93039041f08c5c006f17942ad1849
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 13:37:30 2016 -0700

    another typo in README

Tools/C_mk/README.md

commit 315c35f12aee4ea2af48be37a2b232b3265d1c44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 3 13:34:43 2016 -0700

    typo in README

Tools/C_mk/README.md

commit 6e81196ef418b06a7662643e1df4f00e422d482a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d1366e054df9e2bdef2031b6249cdddc2dbe484
Author: Grout <ray.grout@nrel.gov>
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 5ae09d854e18984117afeef427b873df667c2c9d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 15:34:12 2016 -0700

    set default header formats.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit 960953503702f956e35557a8e47830d08aacf4a6
Merge: b0f22fc a5f35cd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 13:36:45 2016 -0700

    fix merge conflicts.

commit 46e8ce25b57a8d2aa08ee08dea0095ab0dd47426
Author: Grout <ray.grout@nrel.gov>
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 b0f22fc1806df57fc89326b1338996a39943e137
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 2 12:08:34 2016 -0700

    changes to doc and inputs.

Docs/Readme.io
Tests/IOBenchmark/inputs

commit a5f35cd2559f3a4bd7484df36435e4104b945a66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5e06d0cb73d24f009c040ec4d6204a47b626baef
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 1 16:37:18 2016 -0700

    simplify file order reads.

Src/C_BaseLib/VisMF.cpp

commit a1c492a30c8d6529e655fe2a664a03a8c242b38e
Author: vince <vebeckner@lbl.gov>
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 3929b37f98c3c0aedf5eaa93ab972a76ccdc06c1
Merge: 2fa75f1 ee93a0d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 1 12:31:57 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2fa75f1acd09a9979d8ab044a7e0878c235be2f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ee93a0dce616a01658e642a891c8777e142e59eb
Merge: a86a954 7f461b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:17:51 2016 -0700

    Merge branch 'development'

commit a86a9544ebd0c8454935818037088372ba9218b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:17:28 2016 -0700

    Release Notes 16.11

ReleaseNotes/release-notes-16.11

commit 7f461b4cc2cba860a1bff90ee1561c653e61b0a9
Merge: e0abafc 7ae9f9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 1 09:16:50 2016 -0700

    Merge branch 'master' into development

commit 0b132625a9c94f3c9882b8cfcb1a9c8edd647429
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e0abafc574b98a2f1abdd0b6fbeb4620ede988c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3daa965c6f0b777d5306a4f2aee8c4ba43a0afa4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9ea233a077380fe7a9608805b121accd19030dda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 28 14:56:59 2016 -0700

    minor

Src/C_BaseLib/Box.cpp

commit 986c5ef7cf561922f090e061adbefc053f402707
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 28 14:48:44 2016 -0700

    optimize sync reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit af5db3ea9fdcd93a60d14998a0113738e98573e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 28 10:37:02 2016 -0700

    fillpatch for face data

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90

commit c8f268411d9cc96d5e321f3cccb70794ae535ddf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 79bb66193ecfa5ef2e32e4e76b36621755b9a0b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 27 16:21:43 2016 -0700

    Last one ...

Tools/RegressionTesting/IAMR-tests.ini

commit 04554663f918deb8bf80e8e2ceacfdc6ac8db82d
Author: Ann Almgren <asalmgren@lbl.gov>
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 d0bf9427540600afc1059698a8004c34d880ac4c
Author: vince <vebeckner@lbl.gov>
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 2b3c39a2a32834443ced697e8951d911b933d05a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 27 15:39:37 2016 -0700

    added const.

Src/C_BaseLib/FabConv.H
Src/C_BaseLib/FabConv.cpp

commit 342786427143ce193df6e2b28f8b546aab718ee7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 27 15:38:54 2016 -0700

    correct comments.

Src/C_BaseLib/FArrayBox.H

commit 4e137b69ee4dd84e083d2720ea329c9aaccd3935
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f0a23f738403bafe6022b117a66016ae68c1dfc4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 27 15:26:05 2016 -0700

    Removed Nyx-tests.ini from the regression testing directory.

Tools/RegressionTesting/Nyx-tests.ini

commit 44a3642d2b90b202459fc466488826eb3c5a56ef
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 12:26:21 2016 -0700

    change to a more searchable name.

Src/C_BaseLib/FArrayBox.cpp

commit 8ff36f474ccc768e0a700060e4a902becf1c1bf0
Author: Grout <ray.grout@nrel.gov>
Date:   Wed Oct 26 08:28:41 2016 -0600

    Fix to make InitOnePerCell work in 2D

Src/C_ParticleLib/ParticleInit.H

commit 10bdf7581557c6945f68ffcddadac63706a39596
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 24 15:33:45 2016 -0700

    make sure grid id is valid

Src/C_ParticleLib/Particles.cpp

commit df65a1e9b7600e49c9628f7bc16539ec72242f26
Merge: f187776 a5f4e52
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 24 15:22:28 2016 -0700

    Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio

commit f187776d093519fe960b36445acdd7102ce9073d
Author: vince <vebeckner@lbl.gov>
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 abee2b73d6e21f4d628ff8036890196b578e6313
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9a24a266a57b492801c5bdc19b72621ff290457b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8836175dd07c151789245713cdcf814f7500da55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c281f77b1e31aef45478dcb364b05237e046bf92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 daec9e6a51a32da55d81592e11d964c04768d327
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e910501621a52362c74b06378bf42238adfceb5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ed29bfc8d31c3087339e5759a4b729a1d951d7fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7882d0bbffeb9a543d5ad29b6ef7f14c4591b56e
Merge: 339ebc9 50fd0c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:43:52 2016 -0700

    Merge branch 'development' into amrcore

commit 339ebc94761ea312dd484da8c474c1cac04ee036
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:43:45 2016 -0700

    minor

Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp

commit 7ae9f9e85ae7a6c09296fbac413aff8849b6131b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:07:36 2016 -0700

    add missing template parameter

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/MultiFab.cpp

commit 50fd0c77302e9dddf82768a35a92c3a5eff57e7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:07:36 2016 -0700

    add missing template parameter

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/MultiFab.cpp

commit 5859154ed48c7d46750a798de6a2235836546bcf
Merge: ae0e394 6dd04a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 20 16:03:18 2016 -0700

    Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore

commit 6dd04a593b0cc0e956bdbd5b3ce06850cf967b6e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:06:59 2016 -0700

    Getting the cmake stuff to work ...

Src/CMakeLists.txt

commit 4bd890b701a8eaec1cca4e168073a2543a809937
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:05:50 2016 -0700

    Rename box_camr --> box_camrcore for C_AmrCoreLib.

Src/C_AmrCoreLib/CMakeLists.txt

commit 6f07d1dc6ab4d331e28250df20f716bdc54247b2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 20 15:00:46 2016 -0700

    We want AmrParticles to depend on AmrCore not Amr

Src/C_AmrCoreLib/AmrParticles.H

commit 88b3a24fbf41dbc457cf384d5a9df23ea1e8ca7c
Author: Ann Almgren <asalmgren@lbl.gov>
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 ae0e39483fde5cf3d49430f9f36287110783915a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 20:48:33 2016 -0700

    minor

Src/C_BaseLib/PlotFileUtil.cpp

commit 7b81d83a97977208142114e242e4d6cc3639662b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e42d4f6aac796560a1d09c53475ac99c882c85fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:43:13 2016 -0700

    pass explicit distributionmap

Src/C_AMRLib/FillPatchUtil.cpp

commit 1ff582f2f16834f0c66e50e1a96e359c685cbc55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 16:41:46 2016 -0700

    minor

Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp

commit 2e7a8785fb459a82bd82a9135e147b2ad710c5a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 13284b2ff42dc4ecb3ce68d40d4cc17daee8ea15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 71e1618772de65d9cc75ec7f1e11f4d52d07e6b5
Merge: a2b39dc 36ba7c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 19 17:16:29 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit a2b39dcfd29190de72e8f218f1929962e2891618
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 36ba7c1e93f824e715a7d2d88bb6e28a921a897b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 19 10:28:55 2016 -0700

    fix a typo

Tools/Release/ppCleanup.py

commit cb7e2b4ce415f7416b5de560059c00675d378510
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d57496744b12ba7cca056dbbf0d9e2fa4d84ab44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 82dca060736d9d15494a2a45effb57c63cd7d22a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 450c8c2ce46c559361cc50b9741d2a511d5635ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1de7f66285b0970fbb9911daad6d244b8620b62f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2d1f11ea1a0a58106b87bfa17b6690011a5fa1ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e1f2f80607ba3eee58711d88ec9f84d985170575
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e990765c5c27ff8dbc193576103ee5d93d8e1884
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:12:32 2016 -0700

    new BaseFab::make_alias function

Src/C_BaseLib/BaseFab.H

commit 7f962893dfdba8ce2272cbfd5cd9983089dd4616
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 16:12:32 2016 -0700

    new BaseFab::make_alias function

Src/C_BaseLib/BaseFab.H

commit 8b7606532a7c0f4db1b4b336d72b46e6db91dce9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5fe3a97d2b21f0bb464bac48b28f4e05748eee15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9050383ea90f974da451516db70bcff8db9bae05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 59e2c1b4472302e400afed55a112d997b679ef01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 10:28:36 2016 -0700

    remove unused variables

Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90

commit d3aa0bc6769301d4263919da3d0d885693c2e3e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9de3d8c163f4aa5f939dfb1ef03ccbfb67bc350
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3e5e27631afa36b23444ad54742452a8695f2c2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 19445c76e190b9498aa9baaff4eae6b449fec57a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 773ac23ecca15476bf45c055e0f061055a129688
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 05abd40e9bb03373d399d5429094c6e3665be604
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 beb75b32a6c383cb792be0ffbaf84eabf448fefb
Merge: 8075a32 9a8abe7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 14 15:55:58 2016 -0700

    Merge branch 'development' into amrcore

commit 8075a327e86c2a5bd78db4fb31d3f64e24714711
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 428e613719e373de266f6129bede28f57d5fb2c4
Merge: 9c41ffd db02f7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9c41ffd16d669ba09950ff6dfda4913d26d95102
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9a8abe7d2960e3c44d865c3794f5047870525981
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 13 16:00:06 2016 -0700

    using std::isinf & std::isnan for GCC >= 5

Src/C_BaseLib/FArrayBox.cpp

commit 86d93d88b8130281b0a55434c328e6aeb977fc6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f45fb5a6d12f73099bc3c720b4d6990b0c5927c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 13 14:59:52 2016 -0400

    some updates on the suite

Docs/UsersGuide/Regression/test_suite.tex

commit 2c7054da06d161d5fd0ae98c6e0e9ed726616c2e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 13 08:32:43 2016 -0700

    Minor mods to README to point user to BoxLib User Guide

Tools/RegressionTesting/README

commit db02f7e481b1d23022724500e81d3d9ea0e85a2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 09fe908919553109b0939a057beecd1f0e803fc9
Merge: 3c1a07a 131eca7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 12 17:58:53 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 3c1a07afedfda2468716f77febe35d3852e706e0
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 12 17:58:24 2016 -0700

    Add more info in the RegTest README

Tools/RegressionTesting/README

commit 131eca70163b71a58aebab7ce14653bc82d18cab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ceb1e1241ed8e71ab355388dab116652fdbb9099
Merge: 2998727 599057c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:12:13 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 29987274f3899c132cbe7e006ae4e8b648a8e5d4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:11:33 2016 -0700

    fix typo in profiling call.

Src/C_BaseLib/ParallelDescriptor.H

commit a5f4e52bd92a11ca5a1fc2f533d9fbbaf7de26fd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 12 15:09:43 2016 -0700

    fix typo in profiling call.

Src/C_BaseLib/ParallelDescriptor.H

commit e3995e0a8fb944a1a1a1cd87da9218af67a0520e
Merge: 6821c17 599057c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 12 12:44:38 2016 -0700

    Merge branch 'development' into amrcore

commit 6821c17f7fd4d8d502d36e4369c24eaaf58dcac4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8edfc208ce60e4c47e6094194292b7feed89759
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 599057ceef6d7191a887385dafe038ce349f7ef2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e154eb2f0a51f8415318d44bc8b3b180078a89ee
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 12 11:16:43 2016 -0400

    make the use of the f90_preprocessor optional

Tools/F_scripts/dep.py

commit 2389ad3fbfacba6d8a311321a36ce6bcb934acec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 12 10:33:20 2016 -0400

    module matching needs to be case-insensitive

Tools/F_scripts/dep.py

commit 95e4493c575a12296eb6225c8b97b438adef5db7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 067597517a762c7c4d9e353122be5733e5d262e8
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 11 16:27:40 2016 -0700

    set checkpoint and plot header versions individually.

Src/C_AMRLib/Amr.cpp

commit d9101c31721cd02a28d2387baf19651734a9b3a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5848ce51681c48632b705a624f8f1cbcf3b27c79
Author: vince <vebeckner@lbl.gov>
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 8c2711bd64915900f675674437ff961edc9c8b8f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 11 13:05:29 2016 -0700

    fix for faminmax header.

Src/C_BaseLib/VisMF.cpp

commit 9f8d37ddafc3f2c657f7a892664527f8bfd7ceac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 11 11:19:10 2016 -0700

    particle: minor

Src/C_ParticleLib/ParticleInit.H
Src/C_ParticleLib/Particles.H

commit 7f3b1d48760a9bbc66a128d49edaeb65c81ff71b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 13:38:00 2016 -0400

    fix dupe

Tools/F_mk/GMakerules.mak

commit 97ff7e99f17b0f3f41665d9c12d1340b859a9c1c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 38213faf3004b58ae451ddea80d4839b54903f64
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 11 09:48:56 2016 -0400

    clarify where EXT_DIR data lives

Src/C_BaseLib/BC_TYPES.H

commit 8281f3c8e13035ec93001eeec2027fcee7eb9892
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c83e139cb281cfa7aad0fcd5487bea46db00cbcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 13:37:39 2016 -0700

    move more files from C_AMRLib into C_AmrCoreLib

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp
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/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.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
Src/C_AMRLib/Make.package
Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp
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 05c950c1a4efb66110904764998c92ebd15380e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 10 13:13:54 2016 -0700

    start C_AmrCoreLib

Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
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
Src/C_ParticleLib/AmrParGDB.H
Src/C_ParticleLib/AmrParticles.H

commit 659660db1b4400952e80219290da6b14d1bd43b0
Merge: 8009fd2 bc191e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 10 15:58:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 8009fd2049ad972c2f98c5c89b8200b5eb841fbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 10 15:58:00 2016 -0400

    allow for no preprocessing if --cpp is not supplied

Tools/F_scripts/dep.py

commit bc191e4d05ab2ca76dba78b05062116729b4314b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d10d39bcda674f3d9e4421fd30e6e6a3f93c1b57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bfaf8b873eea4a5b486435ffe9878cd48f8e03df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 21:00:42 2016 -0700

    Particle: send the new int data

Src/C_ParticleLib/Particles.H

commit e6e98b2c0c4eee25fd938b6c6aea659414f22fc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 20:29:21 2016 -0700

    Particle: loop fusion

Src/C_ParticleLib/Particles.H

commit 8010a033958143b228c73c69b5cb1dd09e3fb136
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 13:19:23 2016 -0700

    Particle: fix my recent bug

Src/C_ParticleLib/Particles.H

commit 1de010788e9c857827bf77a6caba75a48fced773
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 13:09:22 2016 -0700

    particle: a comment

Src/C_ParticleLib/Particles.H

commit 44bcdaddf1b24daa7be762e21b227f4ff3541582
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 9 12:48:23 2016 -0700

    Particle: skip PeriodicWhere if not periodic

Src/C_ParticleLib/Particles.cpp

commit 54216eb8d92e2cdbc27b7ae6aa782a8d9cc42a31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 22:57:56 2016 -0700

    Particles: range for and auto

Src/C_ParticleLib/Particles.H

commit 28ec6ef3c8b7943f26261811297486db96ea34de
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c6143eb19189f86700ab5bd1ea5b9c7cb053b62b
Merge: 4ce583e 909045f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 19:37:53 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 4ce583e17d655d39ebf846e7226f45d16c82a0f5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 909045fd33bcfc2e9aacc0f5380db6534717ad1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 8 16:29:24 2016 -0700

    Particles: move a few functions back

Src/C_ParticleLib/Particles.H

commit b37e51be6c747d910314d0b80bf5ec07925d8f98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 34eab53f4ebeda602dc0b63c99f84cbc65e3bae3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d57c3166edd9ca74a0f13ea40473892046ce1e20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 2a2334ff95d27ae47f18252b98b35f4aefa496fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 8 15:07:23 2016 -0400

    fix endit

Tools/C_mk/Make.Linux

commit 47ee436eed5a7e78dae8d5534ff05819d4fd5472
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d84c63d19e1e83117f27b3b7003fe9076ddd4c16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 850db1f51c2a83b532abcd92708433cb3aa9a636
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f92c74a66bf102a9774f9c255e63840d01443aa1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c88891c7950f714c5e8f1644cb5e60624399f8a5
Merge: 287553c 5b0ca8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 21:36:51 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5b0ca8f2868cd52593c0a8afb233eeada3dfd4a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 660183d11ce0d419c629e99e16e345962d50aa05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 7 12:31:11 2016 -0700

    add particlecontainer default constructor

Src/C_ParticleLib/Particles.H

commit 0ddb7040c21ac96230f85f95f652cc65c7bc2331
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 7 11:14:06 2016 -0700

    fixes for serial.

Src/C_BaseLib/NFiles.cpp
Tests/IOBenchmark/IOTest.cpp

commit 13ee0c50c04f8cb83f1160b17035d6cebc0b1aea
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 7 10:36:25 2016 -0700

    fix for serial.

Src/C_BaseLib/NFiles.cpp

commit 287553c3df1fe1c119f2e22803b5069f3427d181
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 36f1d3d2a3ca7497fba987e404376ae2c9eda7b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e317783dd4c95d0ada02ecc2f2e1358698d06c4f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6b3971a8f877f006b81370a70beab691262a1e45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 12:31:16 2016 -0400

    require python 2.7 or later

Tools/F_scripts/dep.py

commit 3ec04556d0502d50b244aac19838d7d0e617283c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 7 09:35:07 2016 -0400

    add a few comments

Tools/F_scripts/dep.py

commit 29edebce25f956743c7200ed19afdc3b0028c8b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d3b3495911479b677871c92b4f0e4991fa4fa039
Merge: 49b8bb8 6b403b3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 20:57:23 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 49b8bb8a8513be22204d447a81e12b25732056f4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6b403b3e39620207c013766b340b26611d1290d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 6 17:08:34 2016 -0700

    Revert "FabArray: always respect the wish of nodal flag"
    
    This reverts commit 56f0fb697b1012c5e16b8580f77a72bbf2cd29e7.

Src/C_BaseLib/FabArray.H

commit bd6da391bb6fd8c3b749eea984f802e4141c1652
Merge: 7206998 56f0fb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 19:58:20 2016 -0400

    Merge branch 'development' into preprocessing

commit 720699835f8b90c6ae25a2d0a145046e2aebdae9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 56f0fb697b1012c5e16b8580f77a72bbf2cd29e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 6 16:33:01 2016 -0700

    FabArray: always respect the wish of nodal flag

Src/C_BaseLib/FabArray.H

commit 1b58ab0808122c1a9e12be84e036395f7fc433f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 15:16:52 2016 -0400

    pylint + python 3 changes

Tools/F_scripts/dep.py

commit a659acf61d52ed16fe90814b251b6f29e8449fa8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 15:00:04 2016 -0400

    a little cleaning

Tools/C_mk/Make.rules

commit 254f4181b537af0700fc39c85076002edaf17b73
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f0d36ba124c9f23db71bc38ac6a545c49c0e56e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 13:35:17 2016 -0400

    a little cleaning

Tools/F_scripts/dep.py

commit 9d3fe1dc0ce5084109e404bb4cdd03e95c074222
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 10:27:30 2016 -0400

    prep for preprocessing

Tools/F_scripts/dep.py

commit b70153e9a45497cb6588d54eb4dfcd01e1e108dd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 6 10:05:11 2016 -0400

    make it classy

Tools/F_scripts/dep.py

commit bff0d1558abf41f659dd7c4843f68380f81407c5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 23:04:29 2016 -0400

    add runtime hooks for preprocessing

Tools/F_scripts/dep.py

commit 54a78d8020fb3d117a3db584b2588fb166bbce54
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 5 22:46:21 2016 -0400

    remove dupes

Tools/F_scripts/dep.py

commit 5e771f165c213968f3d65bd528f4e473964c4dbc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7ba91529813c08d9cbc7ff9695ab91c41e51eb42
Author: vince <vebeckner@lbl.gov>
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 b9dd897251827ec219fcd35ac3a820ba826b8939
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b4b8ee8ddba3a710d3f534e5b20047d8d43e3eff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 fceb58b1f8a1221363a1dc2ba43bf4321440a55e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 51818f93bf1bafe48cdb3f85244a5bcf5a0610a7
Merge: a894e90 d373d29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:08:07 2016 -0700

    Merge branch 'master' into development
    
    Conflicts:
    	Src/C_AMRLib/CMakeLists.txt

commit d373d29848fab19dbd175280756ca13b2b0ff8c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:07:03 2016 -0700

    cmake

Src/C_AMRLib/CMakeLists.txt

commit a894e900d21da15a9a81783dd8dfa863b6045edf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 17:01:55 2016 -0700

    cmake

Src/CMakeLists.txt
Src/C_AMRLib/CMakeLists.txt
Src/C_ParticleLib/CMakeLists.txt

commit 4abbc7a9158262616ca41dfe1f68746c908cbbc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:49:13 2016 -0700

    include(PreprocessBoxLibFortran90)

Src/CMakeLists.txt

commit e3902af3778a37493bd8e94fac80d839a01ed5fd
Merge: 3508d11 f60c934
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:30:38 2016 -0700

    Merge branch 'master' into development

commit f60c93463dfe2797e4959286ca179a2bf1a55dd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:30:25 2016 -0700

    typo

Src/C_BaseLib/CMakeLists.txt

commit 3508d11e5fbef2343822e1dfb4efb1aa184fdcd9
Merge: 004bfa5 ff09063
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 16:29:17 2016 -0700

    Merge branch 'master' into development

commit ff09063e57d0ade988e898bfa751c6016ea6fc17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 72c6b91b54cac59ec9527abb8dc2502251c64a0b
Author: Ann Almgren <asalmgren@lbl.gov>
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 004bfa5bc16e568e9e75d6a1456657b20f56fdce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 15:50:19 2016 -0700

    clean up

Tutorials/HelloWorld_C/GNUmakefile

commit 64b4fe89a1e19e4c752e049d7d69110eb28adf3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4bc357fcb4f036258befafd30b55ffaac2055cf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/AmrParGDB.H
Src/C_AMRLib/AmrParticles.H
Src/C_AMRLib/Make.package
Src/C_BaseLib/CMakeLists.txt
Src/C_BaseLib/Make.package
Src/C_BaseLib/ParGDB.H
Src/C_BaseLib/ParticleInit.H
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
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 95a37040793ff1d4946c570cfe69f081dc004e94
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 4 12:57:43 2016 -0700

    Make 1d and 2d versions of NodalDeposition

Src/C_BaseLib/Particles.H

commit 9d1c45d64695d4ba80670106872e94a4d7097f21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 4 08:39:31 2016 -0700

    NodalDepositionSingleLevel only works in 3d

Src/C_BaseLib/Particles.H

commit e0420052a7abec2330e66b6822bd324b764e3cde
Author: Ann Almgren <asalmgren@lbl.gov>
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 8d20a658166e21f17d2284468cc24912f1fbf695
Author: vince <vebeckner@lbl.gov>
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 5745df4a4f0d6e66f4f7c08f4b3bb45c8d899b67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 17:13:05 2016 -0700

    some minor changes

Src/C_BaseLib/Particles.H

commit b732db1929e400685ba2ab61467aada02af32c4f
Merge: 47b975a 42c99e1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 16:34:12 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 47b975a13159bd92f58923553113206cbed80bf8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 16:34:01 2016 -0700

    Add the single level nodal deposition routine here.

Src/C_BaseLib/Particles.H

commit 42c99e11fe8928745b0c5e7b554c8160f3c7b86f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 16:30:24 2016 -0700

    elide some mpi reduce

Src/C_BaseLib/Particles.H

commit 8ece093706ea996b73d8f9220d6ddf81365cfbe9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 15:04:12 2016 -0700

    Particle: use std::array for Real m_data

Src/C_BaseLib/Particles.H

commit a5df41f42f56636b9638becdac78addc7a0ddc59
Merge: 497a57e 382bea2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 3 14:51:22 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 497a57e33cbeebf101c552ec9f1aa7ffb4fddc87
Author: Ann Almgren <asalmgren@lbl.gov>
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 1ef6cef37a5a414e35b798a1bb9a84b090c9fa60
Author: vince <vebeckner@lbl.gov>
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 382bea2191b66e5912e636fa9d9e316c42f482ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 14:07:13 2016 -0700

    update function parameter names

Src/C_BaseLib/Particles.H

commit 7b458502716b13f7011fd26eaf17f473733bb79a
Merge: 389825f 9de54a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 13:58:24 2016 -0700

    Merge branch 'development' into devel-particle
    
    Conflicts:
    	Src/C_BaseLib/Particles.H

commit 9de54a6afedf40aa58c26db900818f8410c283a7
Author: Ann Almgren <asalmgren@lbl.gov>
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 389825f8edfe51268e221901676ce32a631bf3d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 13:48:03 2016 -0700

    white space

Src/C_BaseLib/Particles.H

commit ae589c43b2026502bf5a4327dcdf788719344c41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1af09f5b86a399f87462c9d3aa448ef39db108fb
Merge: b493084 a15e0ee
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 3 09:08:45 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit b493084d55f4adcf61866fd7dfb9047097ad479f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Oct 3 09:08:27 2016 -0700

    update readme_'s

Tutorials/GettingStarted_F/main.f90
Tutorials/README_C
Tutorials/README_F

commit a15e0ee6b043cb87dc99c8fe902b10217eb4fe94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:56:32 2016 -0700

    comment

Src/C_BaseLib/FabArray.cpp

commit 6d2298177821a37a81d36708b98e99a3af69289c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:54:09 2016 -0700

    Release Notes 16.10

ReleaseNotes/release-notes-16.10

commit 135c4b0f1c48ebf7a9b750b329fc4925316a3b2d
Merge: 1af3979 e45a549
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:53:20 2016 -0700

    Merge branch 'development'

commit 1af3979e0a06900a89ca95091df4e676b56bd040
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 3 08:53:16 2016 -0700

    fix a typo

ReleaseNotes/release-notes-16.09

commit e45a5499ed7ffcbdc39852fe1a8127683d932499
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 2 16:13:26 2016 -0700

    Move all of the ParticleContainer<N>::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 b224804c67097af7dbd4767c6064fa55f93880db
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 29 16:43:34 2016 -0700

    more preread headers.

Tests/IOBenchmark/IOTest.cpp

commit a57f79e844b60e77e97bfb0c0c133dea7607bb63
Author: vince <vebeckner@lbl.gov>
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 9347616c69478427f5efb97e53bcce19e0558202
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 898e9535b01c38590b4d7ec39e9b1695baca20ac
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 28 18:49:03 2016 -0700

    setup.cpp not needed

Tutorials/HeatEquation_EX2_C/setup.cpp

commit 6c38b29b2be3c4df63ba8dbf8260933acab579fa
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 697ce623b732ebd9ab8befbdd656e5f4de5a10b1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 264efc7690f1f6514f76bc32fd51c553d11533ed
Author: vince <vebeckner@lbl.gov>
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 a1a4e0a29422bd5cc11a31806aed382dc6eb71c4
Author: vince <vebeckner@lbl.gov>
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 5e81c7f2ce8cc0ccefe8ca7a76d25a8759d3d014
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 28 12:35:47 2016 -0700

    use single write for old format.

Src/C_BaseLib/VisMF.cpp

commit 848241e61a2fd33e022a6b76d924e4fdf19d90d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:14:55 2016 -0700

    fix comment

Src/C_BaseLib/Box.H

commit 3b227094fcfdd476390a1f324ef0dedbdab8a188
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:02:28 2016 -0700

    comment

Src/C_BaseLib/Box.H

commit 1dc4b2fdf8b43a9d7a27691bb3328ca47bac1494
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:02:19 2016 -0700

    minor

Src/C_BaseLib/BoxArray.cpp

commit 2398bf92c336f0ec991473eecd569d70817278e9
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 27 15:42:11 2016 -0700

    fix for combined transfer.

Src/C_BaseLib/VisMF.cpp

commit 27195c7d8c32f39337d7848f76e8953ad4b63be9
Author: vince <vebeckner@lbl.gov>
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 3f5f0407f3908f58dbba1210463590c79c542afd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 08:15:17 2016 -0700

    nodal SumBoundary: forgot to zero out the destination

Src/C_BaseLib/MultiFab.cpp

commit e2597f80c558e2f3208802a644709a21becfb4e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8bdd7f55a6a533d9d4c5c6c3efc8b22402957d5d
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 5b44f9e2deadc533c772e6e242e368bddfd83fc4
Merge: 55f38b1 1e86e03
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 26 13:08:33 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 55f38b14539998b80bfa947f15f427e1d7452bad
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 1e86e03c59cd4be4acf7be85df644a8779801758
Merge: 6218888 e28d9d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 12:06:25 2016 -0700

    Merge branch 'weiqun/SumBoundary' into development

commit e28d9d3d664461491b3167bc9162ad853bb3de18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 11:29:01 2016 -0700

    SumBoundary: fix new bug

Src/C_BaseLib/FabArray.H

commit 1a8c1d0fff390f31aaba4a151208f0964ed931d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6218888079cbce611f5b74c8165e262b6ec571e4
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 70c8d6b0d3f29abb33294ac190983c043a8a14ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 291aa8c68a6a6a768504b11b24ce9e2886b37151
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 08:37:50 2016 -0700

    typos

Src/C_BaseLib/IntVect.H

commit beeaeac1c6765c90734de91fad2ff9216517c728
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 25 18:16:49 2016 -0400

    add -Mbounds for PGI in debug mode

Tools/C_mk/Make.Linux

commit 8078ce585b55b263b2b4e53fd101aba55fc0caa2
Author: Ann Almgren <asalmgren@lbl.gov>
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 3938fd4ea859ecc3fb2c727e3af1f9ad6fb62675
Author: Ann Almgren <asalmgren@lbl.gov>
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 153adb24468cd047c27f805a3915a6292db4ace1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 43ede216114719f0a04c26c50117d85fade8c94f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 1bca1789ee917f89515575d817fe0f40d0c626f4
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 215c3e9861d5b7c05c7c7453ef99964cf4cd4a12
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 5b5ae8cd578ac5ce04c5d6402bf640e792f681d1
Author: vince <vebeckner@lbl.gov>
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 b724d19864b0390055ebee0dbedaee6baa771d6d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 15:15:12 2016 -0700

    added io parameters.

Docs/Readme.io

commit 4693c8bc87918d7853b8b1e4542e602e83d19b6a
Author: vince <vebeckner@lbl.gov>
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 defe644d85833fb68019d605501815dcba64385a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 aa3c10f9929510a7cb52c95ea7707c6c9bc4be1f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 b6075e912cbcbc9bfbb364492acb2e18365e6e4c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 12:15:24 2016 -0700

    parmparse inputs, change defaults.

Src/C_BaseLib/VisMF.cpp

commit 2459c7dca86cb59b724c4a01275ad7c67c1b6099
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 23 11:03:11 2016 -0700

    set passed options.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/inputs.dssmf

commit c358d4ce568943b1f98c6d395b9edec1ae7cfe1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 22 21:19:15 2016 -0700

    This reverts commit 47834f6a346.  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 0266192b5e2826f5d559b2ff60e0cc70a334a199
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 22 18:12:55 2016 -0700

    Cleaned up Tutorials/PIC_C/GNUmakefile.

Tutorials/PIC_C/GNUmakefile

commit 47834f6a3464d5b6d0d966d99323c2f5f37b639d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5461e2270a766f51a7cfc3670e26721bacc322db
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 22 11:51:57 2016 -0700

    added setting for synchronous reads.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit aeb3dc5157dbaba8cb453e0afd5f78650c43096a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 d05a83891536b8b17a57538eeaebb93b7e24209a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 3e5624a4fcb69342d295a3f11d3f8338512cf8ac
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 102df475d42883d9e2b78ea062b491c4c6d911ff
Merge: d071ee7 9fadf67
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 21 13:24:01 2016 -0700

    merge fixes.

commit 769c01c3e23205408c368079da556977460a01cd
Merge: 562ed98 807c70b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 13:17:07 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 562ed986b53f4549411be1ada8013399c58fce2f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 21 13:16:18 2016 -0700

    HeatEquation_EX1_C to uses PArray<MultiFab> now for the state and fluxes

Tutorials/HeatEquation_EX1_C/main.cpp
Tutorials/HeatEquation_EX2_C/main.cpp

commit 2b4b2c716fb611cfdf95a31a5eaabd1dfdcbc87a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 807c70badaae8964d12ea3f945dda2c173f32b23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 09:06:28 2016 -0700

    move User's Guide from Docs/ to Docs/UsersGuide/

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/subcycling_algorithm.eps
Docs/GNUmakefile
Docs/GettingStarted/GettingStarted.tex
Docs/GettingStarted/VisIt_2D.eps
Docs/GettingStarted/VisIt_3D.eps
Docs/GettingStarted/edison.run
Docs/GettingStarted/edison_omp.run
Docs/Introduction/AMR.eps
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/Introduction/varden1.eps
Docs/Introduction/varden2.eps
Docs/Introduction/varden3.eps
Docs/Introduction/varden4.eps
Docs/LinearSolvers/LinearSolvers.tex
Docs/Preface/Preface.tex
Docs/README
Docs/Regression/test_suite.tex
Docs/Regression/testsuite.eps
Docs/UsersGuide.tex
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
Docs/UsersGuide/Introduction/varden2.eps
Docs/UsersGuide/Introduction/varden3.eps
Docs/UsersGuide/Introduction/varden4.eps
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 6d1e8e5c75b1b795e049f428fd3744b500f2ab0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 21:08:47 2016 -0700

    PhysBCFunct: for clarity, add empty destructor

Src/C_BaseLib/PhysBCFunct.H

commit e980cd1363d4b53f949ab61da62849ef6e69a5a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 20:53:16 2016 -0700

    HeatEquation_EX2_C: use preprocessing

Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit db9e5b2bc3a19e251feae2c1107b381f473ae458
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 17:44:06 2016 -0700

    HeatEquation_EX2_C: fix call filcc

Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90

commit 55b008cf77dcb29ff7baaed2cb07e836b42946a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 17:27:23 2016 -0700

    HeatEquation_EX2_C: clean up make

Tutorials/HeatEquation_EX2_C/GNUmakefile

commit 90dd2a0141eebe0b6ef87bbd0bb411a50563bbc4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c57f6c8d922e9d618888469055a67fd08b60366a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6029ac65d1bd6956fec001f4b48ef7bf53d3629a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d071ee705485c879dcac3db5a2e52f39d945b3fd
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 20 15:53:13 2016 -0700

    just use sends for now.

Src/C_BaseLib/NFiles.cpp

commit fa3d491edbb8313053cbb6a0ad02d29f285e5387
Author: vince <vebeckner@lbl.gov>
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 9fadf6768dd63c4b30a9d3bf1cca313569344060
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/FILCC_1D.F
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/Make.package
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StateDescriptor.cpp
Src/C_AMRLib/bc_types.fi
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 6862211293ed9882e8026e285b44f9031e330a8f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 20 15:34:22 2016 -0700

    remove check from timed block, cleanup.

Tests/IOBenchmark/IOTest.cpp

commit 951bd837c673743fe77a161490da3db1d0083bcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 35b74d54465e2611a8e867e41d391ef82e6d8ab5
Author: Ann Almgren <asalmgren@lbl.gov>
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 70fdfcd53c9ab4079389e22cf797cc179f5e6fa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 11:09:30 2016 -0700

    make it compile

Tutorials/HeatEquation_EX2_C/main.cpp

commit 7eb4d971e46696b69b2029fa67b9d6642a1118f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:54:14 2016 -0700

    minor

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit 1e56dfe1a338b52b835130da54a56e7a31f007fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:53:45 2016 -0700

    add default EBASE

Tools/C_mk/Make.defs

commit 58640777a059c4995e694f9bfe1637a2fd668729
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:37:47 2016 -0700

    simplify GNUmakefile

Tutorials/HeatEquation_EX1_C/GNUmakefile

commit ecce81e41ccb4e2f8c62f2d6158d002d6ea42ca6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 20 08:37:33 2016 -0700

    move the rule for building executable to the top

Tools/C_mk/Make.rules

commit aa5f86c948591999736d0da0a4abb4c2b8059d1e
Author: Ann Almgren <asalmgren@lbl.gov>
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 45bf6b4da70a50e48099cdbba3e102650294bda2
Author: Ann Almgren <asalmgren@lbl.gov>
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 d5315b51e93dd09b0a5fac80c577289cecf98c5a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3082fef8cbcf764949f2374ece24729ff4b6626f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 517528be279b807fa23bbe4bff2808046cc4fc20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 21:16:05 2016 -0400

    add new example

Tutorials/README_C

commit 6e2b82016dc12a69d7691273a2d84329fb8d9259
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 21:14:13 2016 -0400

    get this compiling

Tutorials/HeatEquation_EX2_C/GNUmakefile

commit 2ec86d8f18b510bed0bd32c3fe6fb20632c797b3
Merge: db82c04 24d4f9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 20:58:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit db82c041c58ccaa4c69c2bab804dce3a1719955f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 24d4f9bad5d2354d6de217fb93501065121bfd86
Merge: b118d0a 94d13f2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 17:49:51 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b118d0a03cdfaaed0660e56b66f0a5705e65eb1b
Author: Ann Almgren <asalmgren@lbl.gov>
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 94d13f221a7986750a515ee57cf7ed783c5edd32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f799329c5de18a3a4dd0ef70ffff1ddbd2990639
Author: Ann Almgren <asalmgren@lbl.gov>
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 7941c772ece5f5c533db815ae3b47809190f4b87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 19 14:44:41 2016 -0700

    add FluxRegister::ClearInternalBorders

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 6285e8f8eaa6957fef0c60283f812ca509963430
Merge: c646bff 13cdd52
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 19 12:59:47 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit c646bffb266e086bc1d0c867fe0e156f498ea9cb
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 ae20e7de5d32047eded9616a6a3bdc21771e2062
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 12:48:17 2016 -0700

    fix for special case.

Src/C_BaseLib/NFiles.cpp

commit 13cdd523167eb13899cfd59d05f31a31d7dc03ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 19 12:36:20 2016 -0700

    FabSet::plusTo (a MultiFab)

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit 7e1160ce3ec4c575470084e8b17443ff5527bfc5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 11:49:06 2016 -0700

    another test inputs file.

Tests/IOBenchmark/inputs.dssmf

commit bafc22d746e03db9ed17617757e863a90aac912b
Author: vince <vebeckner@lbl.gov>
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 38c55fde144f2c43138224d4d88d7810f0e717ec
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 19 11:39:54 2016 -0700

    check that the written multifab is valid.

Tests/IOBenchmark/IOTest.cpp

commit d33b66744d4451aebd1dcbc36a173b997bfd3ae6
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 3f0e3b74bbf34f2cca14ed6dda5518ce0e56945f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 98544711715252e19b0fd45fcc8074225ee0ec75
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c44583c55bd24484f3536132a465fbad73f06f3f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 19 11:30:24 2016 -0400

    start documenting tutorials

Tutorials/README_C

commit faaaa5d8c258379109f3dfae68c0e914d244cd5d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 15 17:39:00 2016 -0700

    new test flag.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 0eda9c50ecef6502af3d993d3b85013c93a00eab
Author: vince <vebeckner@lbl.gov>
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 3c0e404e131d8edae6156893836a40faea65ef71
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 15 14:59:22 2016 -0700

    ifdef for serial.

Src/C_BaseLib/NFiles.cpp

commit 583adec092f41a5f9d81007c578e7107f90489d3
Author: vince <vebeckner@lbl.gov>
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 aaca2036ead9a0cc785b5719d9165241a8d5f0ec
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 14 17:22:11 2016 -0700

    update test check for nonzero decider.

Tests/IOBenchmark/IOTest.cpp

commit a5d1c04f3a8edaee838e508aaa544db07e4f25ad
Author: vince <vebeckner@lbl.gov>
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 8c3930ad12c53e493924a696cfc6e7c9e7390a93
Author: vince <vebeckner@lbl.gov>
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 07060ff938508cd6f70654991f8b7890db49f4b5
Author: vince <vebeckner@lbl.gov>
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 e1aaf0e8e6ddcf6cac214d94806917b174ae2d0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 12:41:45 2016 -0700

    remove unused and misspelled variable

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit 603dc7c88cc696f97cb819c8c1e16344257d142f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 08:57:39 2016 -0700

    use dot product to implement 2-norm

Src/C_BaseLib/MultiFab.cpp

commit 02e9133ec86b98f3ec7caaa1493f71c3166be713
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 08:57:16 2016 -0700

    fix typos

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp
Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 8b352a6a183513711fb454ef240a075bb04dd91e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 17:36:20 2016 -0700

    clean up comments

Src/LinearSolvers/C_CellMG/MG_3D.F

commit 8cfba06dff661eb202244916ced1305738f05b74
Author: vince <vebeckner@lbl.gov>
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 1dcbfd685f07dc6e66e052a6f5dd444ed80332ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 02998ec6e870aae89d64afe1597b777a5214185c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2ced6d48b01bce76023de397af7bf442f4e4388a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 16:07:09 2016 -0700

    C_TensorMG: cleanup

Src/LinearSolvers/C_TensorMG/DivVis_F.H

commit 4ec71cabdab36b47ce1d2fa0019dbd046c2355ae
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 16:01:46 2016 -0700

    fix the special case.

Src/C_BaseLib/NFiles.cpp

commit 1db87e4d134d5cc7c9ac8c2955c3b68c7004c9cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77ca7a8b7064038ba3c01c5a432e836c311260e2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 13 15:51:42 2016 -0700

    new iterator tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 5f0323af8337b6f3c027eb939feb1bf63ceff4d5
Author: vince <vebeckner@lbl.gov>
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 37400d928cc002f4911ce5123e1cd229852830c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6082ae6b2fe8ed80951ea61ff30f6bf829e1af2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7ff2fabf1e29cf35742307f08eb48469c9c78d3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9d988826ca3858ced89cebcd1232da142c86f79f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:40:15 2016 -0700

    omp in C_Tensor

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit e2971deb5b8e07e6dcfb98b4926c64b51cdec8a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 14:34:56 2016 -0700

    omp in MCCGSolver

Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp

commit 9779ef992d5ede03ebd9f1f67220abc0d31d5750
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1f9a1e5e0428131079217699b52ec736ca5e6973
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fcb941e4e11c6c03862bc761d68567ad7a4a1ada
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 82acf67443dacb2355eb62bcf62b8f86118e4138
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:22:41 2016 -0700

    CGSolver: use MultiFab::linComb

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ff4ce5e573862bc673b42eafec7df05cc27c1097
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:22:16 2016 -0700

    add MultiFab::LinComb

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 65f4fc450ee29346672ff62745468c466c7dcf80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 13:10:38 2016 -0700

    BaseFab: make linInterp call linComb

Src/C_BaseLib/BaseFab.H

commit 4677a543d507612f335a5078c5b6ff2f70564e68
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ac7900445f36cbc141b72895871e6a7f44797646
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 13 10:30:47 2016 -0700

    BaseFab: fix new bug

Src/C_BaseLib/BaseFab_nd.f90

commit 212608799a59a7ef3fbc2f3bdcd92d019eef3b9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f002e1fd0567c3c0d7edce8ca6b74d05ba543ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fe3f65c640cff8e25867a7b010002077270e7492
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d247ef8080b477ed9ff426f3c5b0daa740bafc56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e59c5b210d79a23d65131eab737ebe286572d3d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 89bcb3d6fe30a820a9423e8bbd44aa52bbc64a81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8f86cfd2af8370bf31b04f5ca63169c6d5d2b871
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 73bf0e7c584bdeeff879b4e6b8651e6e4fc3e17a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e5db468e3630f867320961df786731adfd782a7d
Author: vince <vebeckner@lbl.gov>
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 b0326d182fb86c1b02d7a1166435fc8ccf65cde9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a4a3997267100128b15e877e85eb2be84a2298ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 69b6d74afeaf4148bb123bc0086acf55e1be3072
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 12 11:19:27 2016 -0700

    add vpath %.fi

Tools/C_mk/Make.rules

commit 94178a0787f23f8f5656bff4aed028c6f6f64744
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 519e8ee1d5de71bce8f0f39f9d2d53495ca18a76
Merge: 2d31b05 2ea1f8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 11 10:02:50 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2d31b05fd80b37cfef087fb266afa773a3b6a842
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 11 10:02:37 2016 -0400

    new inputs for the merged castro + radiation

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 2ea1f8acc0ec1ababa04f6ab5dbbed9230c255f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 14:52:51 2016 -0700

    omp in TensorMG

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit ef975d342b79974fec903b4294480ee4667736c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 14:19:32 2016 -0700

    omp in CellMG4

Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 665580da15f6a50354ea39020307b0f8fccfb971
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:57:02 2016 -0700

    omp in cg and remove XBLAS stuff

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit f9c50dedd4b2e9f553ea2fbd092c2b71ea567de5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:56:40 2016 -0700

    remove nested omp parallel

Src/LinearSolvers/F_MG/itsol.f90

commit d6b582803fa4bd0e9c3579704efb206ba3f771e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 13:43:42 2016 -0700

    fix assertion

Src/C_BaseLib/BoxArray.cpp

commit 70322ab9034b0a6a77704702b9e20087ab30fd46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 9 09:45:40 2016 -0700

    use BL_ASSERT for calls to contains_nan

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 455170e92a6c0f2bec362ce66e292c65406f0860
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ed6fc46764fffd9e5f7d947f48d78a0a5ea7df9c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:57:51 2016 -0700

    test implementation of nfiles dynamic set selection.  not complete.

Tests/IOBenchmark/IOTest.cpp

commit 871455cab87a10e36c3c0a463170018ee2d46928
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:39:58 2016 -0700

    more io notes.

Docs/Readme.io

commit 8ec8008f2d76a1f7add87e84b86b10bcff015601
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:39:27 2016 -0700

    test inputs.

Tests/IOBenchmark/inputs
Tests/IOBenchmark/inputs.dss
Tests/IOBenchmark/inputs.nft

commit e3a879e1b4144001d1875d4f804165d85a373bf8
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 8 17:38:28 2016 -0700

    test for nfiles dynamic set selection.

Tests/IOBenchmark/IOTestDriver.cpp

commit 80dd25c11867536405f813ddfb47feb8bb5248dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:13:08 2016 -0700

    cleanup

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 4f47086c059ead8e99ead7f77644ed123892ea26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:11:43 2016 -0700

    comment

Src/C_BoundaryLib/BndryData.cpp

commit 94330293631b9b0841439b376fff08748ea321d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 17:01:01 2016 -0700

    tiling in FabArray::BuildMask

Src/C_BaseLib/FabArray.H

commit 921326919c1ef7ad80bc13cea710948daac081c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 16:57:06 2016 -0700

    make MultiMask work with multiple component

Src/C_BoundaryLib/MultiMask.cpp

commit c5741be13392632dad771c2ae1fe474a4243d652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 8 16:51:20 2016 -0700

    fix a new bug in tensor solver

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit 1e67f147db77cf9fae0ec42990d6ef66cf697003
Author: vince <vebeckner@lbl.gov>
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 8a9cc08845f8c4958c3cbdc37f98b5b3642ee57f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1dbcdd79c5bad0b80329e9d1a937823e36ae9bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c99d52847d6eb4beefa952405bbf19bd0f03028a
Author: vince <vebeckner@lbl.gov>
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 99e3ee662a47b329a87ceb1258238b15c0af4fde
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 12:07:28 2016 -0700

    use buffer size function.

Src/C_AMRLib/Amr.cpp
Src/Extern/amrdata/AmrData.cpp

commit 006f3e47de291e6c59d70198136e5d5c3b33025a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 11:57:27 2016 -0700

    use buffer size function.

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/NFiles.cpp

commit e71fbb0f5d54c85ec3a485bb29a3350b6a2fedc4
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 7 11:55:06 2016 -0700

    use buffer size function.

Src/C_BaseLib/Particles.H

commit 81128c082a995cdbb380c97a192818f5caf708d5
Merge: 3912568 89acb8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 10:02:22 2016 -0700

    Merge branch 'development' into weiqun/multimask

commit 89acb8e008f1e833efb7fb4638972fae238afd91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 7 09:53:14 2016 -0700

    minor

Src/C_BaseLib/BoxArray.cpp

commit e99605ff30550686ef2264c9b374071458c6df2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 860c18c75f9a7a0c8d55f38022e86cf429cb55ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5aaf35a3f184f7246d75b116f53f03799df523b4
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 6 15:30:59 2016 -0700

    long seeks and separate tags for reads and signals.

Src/C_BaseLib/VisMF.cpp

commit fc66fe206b2b1b27ab57548b2b77d9f9861bf771
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 6 15:28:41 2016 -0700

    updated comment.

Src/C_BaseLib/ParallelDescriptor.H

commit cdca79623bd27b6e90e6ec407d5afb842c7b7d32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 13:30:30 2016 -0700

    fix the new FabSet::Copy: cannot use MultiFab::Copy

Src/C_BoundaryLib/FabSet.cpp

commit 9eb9faef59aed6e2888805becd4c64562ff51dc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6b3de59aec4088b2d3a7277273745bc40bf7f35d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 6 11:09:48 2016 -0700

    BoxLib::match: shortcut when BoxArrays are equal (i.e., ==)

Src/C_BaseLib/BoxArray.cpp

commit 91a1aa1c203b4c9723e6669f13197ea999672f9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a6d4c69cc4cb5a0d8cff091359b693c9d834fe73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 19da91cdad8ef14af6702402b3d1f33a435fa924
Merge: b465833 05926f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 5 22:58:04 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b465833965d0f103119e909551a94d16cfc7eb13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 05926f7ac7ea3e1defac6d8828870eb1b1ceeeae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1b847063e0e5c9446b1f198bc40d31a1e9373c27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 11:09:15 2016 -0700

    minor clean up

Src/C_BaseLib/Geometry.cpp

commit c957058221c8d12607cdf064518af5ccf6355c18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 2 11:06:16 2016 -0700

    assertion Geometry::Setup is not called inside omp parallel

Src/C_BaseLib/Geometry.cpp

commit 102872089e7d570d3740999cb9e761b46c4ee522
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 af3b040bf410bbcc4cd3df6b9d73848726fcd1f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c29d664ae1b9d23d2d570c18428b3e16b54a136
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 1 08:30:29 2016 -0700

    Release Notes 16.09

ReleaseNotes/release-notes-16.09

commit 2ed19502810c534428cf6d68abc14afca948a240
Merge: 1398a3f 4aa17a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8704739908324cd4015bee58491694c2a223804
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 15:44:44 2016 -0700

    close persistent streams before each test.

Tests/IOBenchmark/IOTest.cpp

commit 8bc4cd560afc718f4f1291743c00ea9981eb254d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 14:57:50 2016 -0700

    added more test options.

Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit 44b970156bc22f212c5d61a172f2fa5b0d7a63ac
Author: vince <vebeckner@lbl.gov>
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 839e42139dfc25a08377c9c78b70f80f39552cac
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 14:54:54 2016 -0700

    changed default buffer size.

Src/C_BaseLib/ParallelDescriptor.cpp

commit db95bff08514b9f9c712858187bf0fe1354c9b96
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 31 10:54:26 2016 -0700

    changed default buffer size.

Src/C_BaseLib/FabConv.cpp

commit 1398a3ff80ffd58eb35b75c7a6992e51b4f89761
Merge: b9ccda6 6266695
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Aug 31 13:12:21 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b9ccda63f33fb5fa018a771aa62ff50d81acba19
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6266695a0875133324d03fc44d70fc3544bb4d5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 20:31:58 2016 -0700

    BoxLib::InterpFromCoarseLevel(): fix box type

Src/C_AMRLib/FillPatchUtil.cpp

commit 046cfca3da94c0fd2627955c194088bf2fd4d8e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 20:23:32 2016 -0700

    fix BoxLib::InterpFromCoarseLevel()

Src/C_AMRLib/FillPatchUtil.cpp

commit 1495f9cc268700f33bace73ee96d3b28dfc5ff95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 30 16:47:05 2016 -0700

    add BoxLib::InterpFromCoarseLevel()

Src/C_AMRLib/FillPatchUtil.H
Src/C_AMRLib/FillPatchUtil.cpp

commit efe65a4051078bd048abb0001d032af5e6a13dad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f44eda2d24eaa5063650ba714bb886359b87d9f.

Src/C_BaseLib/FArrayBox.cpp

commit b201405c356509182a5fee86ccdfb924a824670a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f44eda2d24eaa5063650ba714bb886359b87d9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1513952fb063846c7f1f7f5b9d4e0462f27574a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 029754cbb749279ebd33e7e1d70b64aeea82b0f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2127bbb4639a41806bdac6ab42c113492b49ace0
Author: vince <vebeckner@lbl.gov>
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 64411fb997327396c9f15ee0ff8cc7da64ab6f86
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 18:34:23 2016 -0700

    level directory creation setting.

Src/C_AMRLib/AmrLevel.H

commit 72f3433e0920ea315fb07755011bdbb80117ef1f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 18:33:25 2016 -0700

    add more parmparse options.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit d6cff30fb8ff97915f350546692a8312c3fbf27b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f979d9bdc1b53b3c724ce22dfe1d702f4a3dc65e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df4eedff0822d71ae9ed61596fe5fed3cb6eb679
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 15:53:53 2016 -0700

    more io tasks.

Docs/Readme.io

commit 72a4900c43ca27c9058ee4082c0802342ed22bac
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 12:24:07 2016 -0700

    check for sufficient memory for single reads and writes.

Src/C_BaseLib/VisMF.cpp

commit 2f6a34d8ea45fe6b29d763dd597efbaab2d1665b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 25 11:45:35 2016 -0700

    format, set version for plot files.

Src/C_AMRLib/Amr.cpp

commit ebae10cefc6aa9aa07b253ac214cb391b327a40e
Author: vince <vebeckner@lbl.gov>
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 4aa3624f029bc63e127f0d8b4586681d4489b991
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 17:32:35 2016 -0700

    remove Geometry::SumPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 204c107c619e1ef606f210d37898244ab8fa0edd
Author: vince <vebeckner@lbl.gov>
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 37271db05377b25ab92d28a2dd37e5bb73b7b514
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7e3a41b68846bb270ed669599c46be2df5653763
Author: vince <vebeckner@lbl.gov>
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 022d26f337d3aacf7c8d7a54e78281847f9eae78
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 24 14:46:09 2016 -0700

    fix for in file order.

Src/C_BaseLib/VisMF.cpp

commit 226fb95ab85821ab519d547a50d753fb9df402df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2e8c9482249db67f109e40dbbcfd130464f46c02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b2db3d6fe23fb89c7173a931b5d539715eb6cade
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4f17b8fa951304eccdcfc7d03818b457cb05b500
Merge: 9db9e2a 3f38888
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 24 12:21:27 2016 -0700

    Merge branch 'development' into weiqun/work
    
    Conflicts:
    	Src/C_BaseLib/CMakeLists.txt

commit 4aa17a3831426bb3929f8257072601df9f09eb7d
Author: Ann Almgren <asalmgren@lbl.gov>
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 3f38888e230da72cd89142105c294fd1b01cc91e
Author: Ann Almgren <asalmgren@lbl.gov>
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 5987a781bd81329b6ec6c5d162975e7a4b1e7d8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3337f6b321cbd9e59ad2c787fe95f85e3c192db1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 338020123665fa43cee52efc5746a4b18dd4ed3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 771a7133f3afe420fb8ca726d9fa1ce7929ca12e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 23 20:56:43 2016 -0700

    add a non-const version of IntVect::getVect

Src/C_BaseLib/IntVect.H

commit 42bbff243804e2153ff5c7f14a1aae27d9be95a6
Author: vince <vebeckner@lbl.gov>
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 9db9e2af752f361300195dc2516aa071f9396596
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 16eb9f192ade0a4e96b83cd54467a09546a3a538
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 17:32:14 2016 -0700

    tidy

Src/C_AMRLib/extrapolater_3d.f90

commit 709c59024afa8c6b0a29c31bd21270e6209ac917
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 22 17:30:48 2016 -0700

    fix array bound in extraploater

Src/C_AMRLib/extrapolater_3d.f90

commit b0b073f7e0a687ac991858d1e82eb537626e781f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2869a0eb5ce319787afb14a789a661416491bf21
Author: vince <vebeckner@lbl.gov>
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 7ecf7401589fdb825c52125ec665db0b10a61c71
Author: vince <vebeckner@lbl.gov>
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 d80a3eceaf53e380d05a9a5bf4f78fea592bf603
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7f02d46b9b2bbc4870a9dcdf9b08abfa1e60f744
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 12:08:03 2016 -0700

    remove old code.

Src/C_AMRLib/Amr.cpp

commit 98a784a097208d7247f408225c4aadadb38617bf
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 11:59:58 2016 -0700

    formatting.

Src/C_AMRLib/StateData.cpp

commit 3922379dcdabdc3de293e0ab5f07e43b3b74315a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 22 11:06:34 2016 -0700

    formatting.

Src/C_AMRLib/Amr.cpp

commit 80f631d56f4574d2045f98e850426753bd7d5728
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:41:16 2016 -0700

    FillBoundary: return immediately if there are no ghost cells

Src/C_BaseLib/FabArray.H

commit 27e9961bb27077e131a3447c7d09a24c18197f28
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:32:51 2016 -0700

    EnforcePeriodicity: return immediately if there is no periodic boundaries

Src/C_BaseLib/FabArray.H

commit 6a06f33f6961032e8399d9250126fc20df514787
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 23a65ae20f87dbe4994ea6be36ef6af97daf83fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Aug 21 16:01:41 2016 -0700

    minor name changes

Src/C_BaseLib/FabArray.H

commit 6bb1526420b4b134daf9650c85a7c4bc23fe9036
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1c34b28b631a82f13a0acb619de73b7164ea18b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 994a90e816241dc5f4f81450ac0cc71d73619324
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3063f0ded5d77fc834f1dc6b9c355f016531cf26
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 19 15:52:28 2016 -0700

    set relative path.

Src/C_BaseLib/VisMF.cpp

commit cb353640091c8bab3f82405e3340f1b6fb9a2dea
Author: vince <vebeckner@lbl.gov>
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 683fdd229750afd8af15e9b3bc834c3067089e8f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 19 15:50:18 2016 -0700

    more io notes.

Docs/Readme.io

commit 8bb1537fab6f37fe121be1e5bdfcff1c2b38b75d
Author: vince <vebeckner@lbl.gov>
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 c7b76169354bde2bcf2cf33814342d231533b944
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:42:48 2016 -0700

    Extrapolater: fix bugs

Src/C_AMRLib/extrapolater_3d.f90

commit eadafe0c8c8cc41f50e20cf435820b57fac4e321
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:35:50 2016 -0700

    Extrapolater: fix a bug

Src/C_AMRLib/extrapolater_3d.f90

commit 2f6e243b3eead7b494b721d9d8ead6732692bc74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 18 15:07:08 2016 -0700

    Extrapolater: fix index bug

Src/C_AMRLib/extrapolater_2d.f90

commit aff43705290e1003bd114cb7847d5ac6af6466d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c5ced5d457fbc4a8d52c48373d7e1ed5e4c9190b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7ae16f6351bebe9149edc0b5cad06b40204c7e6d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 18 13:55:23 2016 -0700

    removed diagnostics, added timer.

Src/C_BaseLib/VisMF.cpp

commit 1fdcde08b4ace67239ff75660017de65867a2d1c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 18 13:32:41 2016 -0700

    file order fabarray reads.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 20e04134ff9c812709f1a62f5dbe695a231f73d1
Author: Ann Almgren <asalmgren@lbl.gov>
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 b88556c16f24d7446e7b55aa667766b27b77a71c
Author: Ann Almgren <asalmgren@lbl.gov>
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 4fbf9009479bc2f21c081f865e734645f7c052e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 16:35:42 2016 -0700

    new function iMultiFab::buildMask

Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 98b37b9ea69eaca81a9b740fcc97d5cc28520380
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 17 14:35:35 2016 -0700

    changed mf name.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 9e4d7b89737af6d76cd811e750fef0b11c8ff4f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8c332365a9566920273dc7d22ff12033ad6e3fbd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 17 14:15:41 2016 -0700

    calculate header offsets.

Src/C_BaseLib/VisMF.cpp

commit efe5713d0b69d8b6e9ac4bcb700986e5f6e699a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:58:59 2016 -0700

    clean up iMultiFab

Src/C_BaseLib/iMultiFab.H
Src/C_BaseLib/iMultiFab.cpp

commit 08b812a83d613fc13bceb9140b435749c44e0054
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:50:24 2016 -0700

    FillPeriodicBoundary --> EnforcePeriodicity

Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp

commit 1afc15b3cee93b8d28c1b74e6dfb2b964553a7aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:42:47 2016 -0700

    clean up outdated stuff

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 05284ad6fac4ab3b499c8ce750720d0a53773d55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 13:38:03 2016 -0700

    simplify the way of filling boundary corners

Src/LinearSolvers/C_CellMG4/ABec4.cpp

commit 3770ed59cd72b4ccf5e04c6873f04de80f9eead5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1f87a4376542c2a5664f5aa452440708049140ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0f9460c0ba818ae4cefedc8bf37307f95223eec4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 19e13f8a363362f0ce637e4a919ed788ae0051ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 12:14:32 2016 -0700

    add assertion and comments

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.cpp

commit 4e5f268695bb43f4a1a7858a435bf918f30bc8dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a59257d276bcc2b265bc381e6153f60612fde888
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 17 10:56:43 2016 -0700

    fix thread safety for FabArray::EnforcePeriodicity

Src/C_BaseLib/FabArray.cpp

commit 7fb3e909dc30e8689dbfbcd59e94a905e72eb0c8
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:59:17 2016 -0700

    removed old test function.

Tests/IOBenchmark/IOTest.cpp

commit 6324f562ca8bb53083ce69319d64c9a89bcb8f87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9a9cd4734ed571756a519e104fa5f8242a6d433a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:48:43 2016 -0700

    removed debugging diagnostics.

Src/C_BaseLib/VisMF.cpp

commit 00963b39a0aee866e18b7a495fc37bcc40c7fc33
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:45:25 2016 -0700

    added NFiles.

Src/C_BaseLib/CMakeLists.txt

commit c9f95701957190fdaf5e65400b5b69b697ee42f6
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:27:01 2016 -0700

    removed test functions.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 85f4e608db5c05975f94915d8a8853ec2e3daa7d
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 16 16:26:28 2016 -0700

    more notes.

Docs/Readme.io

commit b48bd055bf966b1ef57a26c79d53a6c57b0f8958
Author: vince <vebeckner@lbl.gov>
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 eb3a3fa29a81fe470a14bd8380072eb905a97df8
Author: vince <vebeckner@lbl.gov>
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 5579ba6b3a7751b8182a6d81fe3aebc5ad95241e
Author: vince <vebeckner@lbl.gov>
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 fa6d37a287d82e39a29eef2f8213c933601818fb
Author: vince <vebeckner@lbl.gov>
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 5e055d0d0a42e9b23189ed9206d89ed170ac8d2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4e3bff7cd0811de3b9ce1eb26d3534d6c4e86795
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 15 23:23:12 2016 -0700

    fix EnforcePeriodicity function

Src/C_BaseLib/FabArray.H

commit 9c4546cfbefdadae32191bbd42bcb4787d0f2958
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b9def673244f6e3383acc322fc36c92e97c823ff
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 15 19:01:44 2016 -0700

    combine write functions.

Tests/IOBenchmark/IOTest.cpp

commit 14edacb60a601562938d68836037e55102302802
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 15 19:01:09 2016 -0700

    combine write functions.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 6d81218c8155a61ddf02c53ea9b34231074eaff4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3712af23880eedc967ff68d61c6b36da2127524d
Author: Ann Almgren <asalmgren@lbl.gov>
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 85eda5859c490d179034de8fb4394ebd16c000e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e8551deb8c7bdbfe7a15d01f8993a7ddf2ebca3c
Author: Brian Friesen <bfriesen@lbl.gov>
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 6d0f19d37b5929f35360b220d7ebdb9caa351362
Author: Brian Friesen <bfriesen@lbl.gov>
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 9c63724f8cbe07970e61d2f6bd5c2a8d996cdd5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 11 21:53:48 2016 -0700

    remove unused variable

Src/C_BaseLib/CArena.cpp

commit 6e699ac172bc6d76830b153de5aeee7e1c39a264
Author: vince <vebeckner@lbl.gov>
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 a0b782ef7a9c266caee5ba0d055396bf0bfc773d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 504fc67c5a0a65de47d3d9074d0e827240b79ed8
Author: vince <vebeckner@lbl.gov>
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 d424b89a163736a96b1f99aa0f18941270535292
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 18:24:30 2016 -0700

    added consts.

Tests/IOBenchmark/IOTest.cpp

commit e232c3b8b7137eaf0e1ee89cf5b6b35fe3d988d8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 16:49:48 2016 -0700

    added functions for reading.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 9ef0c90eadd4bdcec22a3e97d5ed304d2656d2a0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 16:46:23 2016 -0700

    added more inputs.

Tests/IOBenchmark/inputs

commit 8ec0a697d7a05faadd94139fd4c3d1c449bf5d69
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 335a2f365a0f07960bd936a146a92ad5de58e042
Merge: 17abee4 7c646ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 14:23:38 2016 -0700

    Merge branch 'development' into weiqun/work

commit 17abee428f7c1f659ddb1cfe1255c49c2e19721a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 13:22:53 2016 -0700

    minor

Src/C_AMRLib/FillPatchUtil.cpp

commit f2b8718bd13a074f48c0779e8d3e095af48faab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d0dc3b9cd4a3392044c43cba68d2bb6a03066a9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7c646acd65b2ce53700b8d04d96a9eb61ad590bf
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 71bca54d650e47d61d5180f9573975a209c54eea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9d59112c89ff5d25ca6cd3e3db8e9ccf6ea1fe5b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 10 12:31:33 2016 -0700

    more io tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp
Tests/IOBenchmark/inputs

commit b82877c83361cad10916ac4f300f80da06f9c8a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9fa0b1d9c6ac43f94a983175913ccce8faac2007
Merge: 2f9dba7 c47bc1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 10 10:53:40 2016 -0700

    Merge branch 'development' into weiqun/work
    
    Conflicts:
    	Src/C_BaseLib/FabArray.H

commit 2f9dba79d58cc4851b182686eb7f40eed94069e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 21:16:33 2016 -0700

    minor optimization

Src/C_BaseLib/FabArray.cpp

commit 2efd0bce04647018f13e8af29680895e5af18e4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 18:13:39 2016 -0700

    fix new bug

Src/C_BaseLib/FabArray.cpp

commit c290274efa30c47e89aa709a72ee1e0db6108491
Author: Ann Almgren <asalmgren@lbl.gov>
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 19f8c921547a7cb99b270d523dba8988a8c7883d
Merge: 5817fa2 c47bc1a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 9 17:42:52 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5817fa28d24c39d00e700421ec2647c43e01bd97
Author: Ann Almgren <asalmgren@lbl.gov>
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 df9064d3b5008a8498729c482df9a9824ce0fc8d
Author: vince <vebeckner@lbl.gov>
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 9cafc7ff4ef6f618823c494fabd50441a1957003
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 17:22:50 2016 -0700

    more io notes.

Docs/Readme.io

commit c47bc1a3b517480a9abd696e75b050fc030487a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 16:13:19 2016 -0700

    update the regtest clean script

Tools/RegressionTesting/reg_test_gc.py

commit b2ab1a535420a92e4b56666565ccf0dcb7138f06
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 15:47:09 2016 -0700

    first part of code for persistent streams.

Src/C_BaseLib/VisMF.cpp

commit f547d641c5923994c7089ec4bf50ce3f03c8fbfa
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 9 15:45:28 2016 -0700

    more notes.

Docs/Readme.io

commit f60dc304fd66510a68d2b895eca8ed72b9024faa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 14:37:14 2016 -0700

    fix new bugs

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Periodicity.cpp

commit 61b9fb3f3406fe46116edf705e7a2f26e059f14b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f7bc27e1864e384b8c6e7db4ea41274c0921c096
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4b66811950d86874d0d62f14e8eb78c7119c8c30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 13:03:57 2016 -0700

    add Geometry::periodicity

Src/C_BaseLib/Geometry.H

commit eb1bef34732b3a442bd13eecb8dfac3704b4fdf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 9 12:58:31 2016 -0700

    tweak FillBoundary interface

Src/C_BaseLib/FabArray.H

commit ccb1da39a108c59e02307dc8a107150ae313233b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e7b2ad9da5049c6a52a69bf980f4747c424e92b6
Merge: 4f30d35 f0f79c6
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 9 11:19:27 2016 -0700

    Merge branch 'VTune_fixes' into development

commit f0f79c622e7ed05bd60c975593c40a14f7cac5ec
Author: Brian Friesen <bfriesen@lbl.gov>
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 d0d0bb985adc085f3443fb98ecd3a47a4cf76b99
Author: Brian Friesen <bfriesen@lbl.gov>
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 e0963ce801e97a6407a73fd4a1e038ab45cce664
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 16:30:30 2016 -0700

    read tests for raw native format.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit af537ec921a2fc2c0299de1d0eca0ac775814cd7
Author: vince <vebeckner@lbl.gov>
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 0bf8a381e9f5b75b1a5dccaf5811bf7ec586c7a0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 14:48:21 2016 -0700

    remove BL_VISMF_MSGCHECK code.

Src/C_BaseLib/VisMF.cpp

commit 0aacc4ffcb787bca982ebf474894e793cfc2bb27
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 14:45:31 2016 -0700

    combine write code.

Src/C_BaseLib/VisMF.cpp

commit 9e4485417ea2b2445d07db022c40276d62cc67d4
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 11:57:00 2016 -0700

    change path

Tests/IOBenchmark/GNUmakefile

commit ad81c9ad25447032f98d9846fda684404af5b0c8
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 8 11:14:30 2016 -0700

    some cleanup.

Src/C_BaseLib/VisMF.cpp

commit 4f30d354e6c93ab01ed4c6f7042d0e9d0ddd048e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 8 07:45:59 2016 -0700

    promote FabArrayBase::CpOp to public

Src/C_BaseLib/FabArray.H

commit 96d02406d0ae2624152b4d40ddbb06917a44a3f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ca53a9419d847cf18602dbcea996d1d458894a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 22:40:47 2016 -0700

    fixed a bug in last commit

Src/C_BaseLib/FabArray.H

commit 1586903107a6b3cc996f740bcb53b69713007065
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0abe0dc606fda31ca58ad27e7bf300fb487e98d1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:51:51 2016 -0700

    some cleanup.

Src/C_BaseLib/VisMF.cpp

commit 551176e7128c73649d55a6b7b7558720eb4d1ee6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:13:19 2016 -0700

    more io notes.

Docs/Readme.io

commit e7a3edeac293cbe20548d618f6a4890cceb2d838
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 5 17:12:18 2016 -0700

    update tests for new vismf versions.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 0a446f8c4f3b07a5246619d068600ddba7f708bd
Author: vince <vebeckner@lbl.gov>
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 1f296878d1d24d0a78c14f603cd545b406806e51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f3bf0fa45dddc1c84f2d1bf41809c4bb8bd04c0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b3b155f7c5c8e2480217a3f24e72824d810f32b3
Merge: 95d4ed3 e4cd60b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 14:03:53 2016 -0700

    Merge branch 'development' into weiqun/boxarrayconverter
    
    Conflicts:
    	Src/C_BaseLib/FabArray.H

commit 95d4ed321cd7eff7a17a77b21e7f96a36cff81a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 13:53:23 2016 -0700

    Abort if FabSet::AddProcsToComp is called.

Src/C_BoundaryLib/FabSet.H

commit ec7a2c889d5841590f58df856744d7b0bde20b73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 5 13:20:37 2016 -0700

    indexMap --> indexArray

Src/C_BaseLib/FabArray.cpp

commit f1ef4361516a9725dc357f498fb4bc0dcd74c140
Merge: 690d59c e4cd60b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 4 21:09:46 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 690d59cd4ebbfa6d9e2682b949b1eea55c85a335
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7e4cff1b06ae297a119cdc69abf58902ebaf977b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 17:27:53 2016 -0700

    filename fix for ungrouped sets for VisMF::Write.

Src/C_BaseLib/VisMF.cpp

commit 235db4f93707ed611d3b548b6ca8ab6613a7add6
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 17:27:09 2016 -0700

    simplify code.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit e4cd60b91cbfe6a1e26259724b734c2ef84a59e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4a3e7f83507f0c02d5ef634d6c5f4c932ada3b66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 16:58:08 2016 -0700

    FabSet: remove aliasing in linComb

Src/C_BoundaryLib/FabSet.cpp

commit bebafa5cd1d2748d7714948f87bcbae35a4ddc67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 16:35:38 2016 -0700

    FabSet: reimplement linComb

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit d14fe5d1ac5e625c0c977efed9442797e7ef65ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 59876f89bfb392da7f91d1a04dbd126af2fa8f9e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 16:10:35 2016 -0700

    use NFilesIter.

Src/C_BaseLib/VisMF.cpp

commit 0d92f380e42a5a5c4448adb9b9f3536996ea44b8
Merge: ed58889 bfbcb58
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 15:37:41 2016 -0700

    change mf to FabArray.

commit 37fa9dd8047ff8b8373f714f56354ba44e62f1da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 15:01:48 2016 -0700

    BoxArray: clear hash bin whenever the boxes change

Src/C_BaseLib/BoxArray.cpp

commit af7e58b9c270fac11b77fe2cd2db056c05645781
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 172db44b074fc12dcf8c2498d6dcc5b672c68dcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7a69fffa8abbe1b5cc32fe46eeb504f9c5a86fcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 4 13:47:29 2016 -0700

    minor tweak of TINY_PROFILE in make

Tools/C_mk/Make.defs

commit bfbcb589334600629b5d58d64fedf269eaf92cc7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 4 13:09:07 2016 -0700

    fixec calls to bl_fortran_set_nprocs_sidecar

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0bce0a16eff0fd595f5da6ff0dc2e4a7764264e5
Author: vince <vebeckner@lbl.gov>
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 022b4ea7807a63e4d659acf394a5f8fbc7dfdd4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ed58889d99b531013a5eb3302824063ddf6f32be
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 3 15:52:49 2016 -0700

    more notes.

Docs/Readme.io

commit 7eedfe01e2566225f0a379ca6f59e416a8aa2709
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 3 15:52:03 2016 -0700

    move remove out of timed block.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 0e4b6ccd426380abd079437a5a498e13c2d05aba
Author: Brian Friesen <bfriesen@lbl.gov>
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 9e2a42713856befcce3c84fca68b991dc75f0160
Author: Ann Almgren <asalmgren@lbl.gov>
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 09daa5baf11f5558eb3d347dd5ebed3b0a20fad4
Author: Ann Almgren <asalmgren@lbl.gov>
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 5045e2da6969915e1b0fa96e74cfee3ce9f0ada1
Author: Ann Almgren <asalmgren@lbl.gov>
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 bf286044245a6a3fa8d99c68492b5bf329ae0efa
Author: Ann Almgren <asalmgren@lbl.gov>
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 be704c847f5a27ed79d9538e077da786c93e0707
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2c31579821f925e4729b207392cf9935801a267b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4665185f92432bf2a2be625ea5140f9f57a703fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e3a06ac8a683a9aaa3e1dd44ba6ee9f002e5f2cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ef7f2ef47eaa28e1553cfe59707650e5f38d3875
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Aug 2 10:13:27 2016 -0400

    fix benchmade link

Tools/RegressionTesting/test_report.py

commit 80963113ad23fbf10a2145dec75f8bebf34318b5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:18:49 2016 -0700

    forgot the header.

Src/C_BaseLib/VisMF.H

commit f81b7d29f7988a87d531fc726197b31ec01552ab
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:14:59 2016 -0700

    test remove nfiles.

Tests/IOBenchmark/IOTest.cpp

commit 910eb4ad6d54774d1dda8deab41dd3ac8a088cd0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 16:14:33 2016 -0700

    tweak set groups.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit f869d1fc31d24fb865c2264e2592a7f3822af67b
Author: vince <vebeckner@lbl.gov>
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 bbb73ed6607dcc1cc58484ee5a785558585816a2
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 12:23:12 2016 -0700

    test group set option.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit dae5118e86cd8df37ba5bff5a7ecb3b74e05426c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 1 12:22:56 2016 -0700

    propagate group set option.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 70965f456daa28015d5cb586d38c9f29ff8d029a
Author: vince <vebeckner@lbl.gov>
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 b0f9447e018ff8b2c5976d6400059b468349c7ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 1 07:26:59 2016 -0700

    Release Notes 16.08

ReleaseNotes/release-notes-16.08

commit 66e00d3159a4d4624eb4b4009917cc7b2838c996
Merge: d57e2f0 328afc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 31 15:07:46 2016 -0700

    Merge branch 'development'
    
    Conflicts:
    	Src/C_BaseLib/FabArray.H

commit d5aed8ce0b2cc272b901f43f59127691f04a73d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 62424b60f3e3f45c9c98c20b385f2faf8bc40262
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2a3ab71877423622fe5a408643bf570c1acabb7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4ee59a3efecaac1018308ae055689148eb544387
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9b0d0d5548a322b9d8068deee0efde0453169636
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 30 10:38:00 2016 -0700

    Revert "refactor BoxArray Transformer"
    
    This reverts commit 4bcb96058ba54850d8a786fef9571bd703821aef.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 4bcb96058ba54850d8a786fef9571bd703821aef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8bf44e84038627112899b4488b7e31cc0898a365
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1b849edbc0eebb8b78281df4ac6aef51a3f3ddb2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a10fa6e460a40b6a950366d412e15a1429fdc9a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4fa35bd0eba7602234f8727174bed0aa4516fe05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fa2dbe1fc367fbed7ab2c73a52a27a7c9279eee1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:48:15 2016 -0700

    updated readme.

Tests/IOBenchmark/README

commit 7a3ad28390271622aca18809cc9a1b280b6df4cf
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:42:35 2016 -0700

    command line option for writeminmax.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 9e3860dbf8ff4230c2dc4fa69ba71b6fd7fc73ec
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 16:27:35 2016 -0700

    calc offsets without communication, option to write minmax.

Src/C_BaseLib/VisMF.cpp

commit 04c7a7dfcc9fb46b7f7a550bcc4353d940b318a2
Author: vince <vebeckner@lbl.gov>
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 355f1c117a9d62b364e122c825c03c30739cd6ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 706471c6ad0127b04d02d7009a47400af26efe91
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 29 14:22:35 2016 -0700

    added stream buffer option.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit deac159078fa90ad3a40181bc08a616734a89b01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 328afc50bb07d82c2ffe47649bbd3d4449324f3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:16:46 2016 -0400

    testnew.py -> regtest.py

Docs/Regression/test_suite.tex

commit f5a5253c29b8b146b5226e222edb3d9a45bbb187
Merge: 052845c f848e1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:11:34 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 052845cdef3ca8ddc2631aa42fbc66cc202718e3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 10:11:18 2016 -0400

    remove the older suite -- use regtest.py now

Tools/RegressionTesting/testnew.py

commit f848e1d70619e6dddb641bf35dac25f6a66b7db7
Merge: 9a7643e 9974bfc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 09:44:42 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9a7643e0c7ef8729836d87a22fd87e2c83379bf5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 29 09:44:30 2016 -0400

    update to point to regtest.py

Tools/RegressionTesting/README

commit 3d9b95b831a9f809ef6ea1359dfc5090948d991a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 57e261630717fcfbadf94fc8417c964952f7e3c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 401f2f6059ab33ebd688f8ef4eedafd2a24accc1
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 17:22:21 2016 -0700

    continue write raw native wirtes.

Src/C_BaseLib/VisMF.cpp
Tests/IOBenchmark/GNUmakefile

commit 0c16b277c1c4a699c294120735118e6f81ea13b8
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 16:54:13 2016 -0700

    test write minmax to raw native mf.

Tests/IOBenchmark/IOTest.cpp

commit feb10d1cd554a3be6bb261960e4edae1fbdb8a18
Author: vince <vebeckner@lbl.gov>
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 04c6cbb4c624eb33fc2d4a97dddd18e377c172cf
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 16:04:52 2016 -0700

    added comments and an example.

Src/C_BaseLib/NFiles.H

commit 9b0c570d1bd0dd13c3917ceac6fb34fb565ca553
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8e1e394e12b31f237c4ca46431ab8a274da36c13
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 28 14:04:14 2016 -0700

    change defaults.

Src/C_AMRLib/AmrLevel.H

commit 9974bfc07d18cf109a153f2c4466f71d4c6879ea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 28 13:00:54 2016 -0400

    a little cleaning

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit 7ef6ca80d8961607fe26085e6be2744b70f92337
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 1228b99e603be1ede13a5cdf6cb2975cb80b5b94
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d57e2f068be95dfcefb6201e60b6118f0ea7fa7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 22:43:53 2016 -0700

    add libquadmath

Tools/C_mk/Make.defs

commit c4a888687905ae953842c2d141d83b0d07ddaf77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 22:43:53 2016 -0700

    add libquadmath

Tools/C_mk/Make.defs

commit 1acd4e1721ec734bd3b179d9388613689b3ff0c8
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:19:15 2016 -0700

    test functions for VisMF::WriteRawNative.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 3f7cc0b4ef8518cdfb1c42a419901670aefba355
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:18:33 2016 -0700

    added WriteRawNative function.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 96127b63d0da230bd0aab323bcd828eeee20b5ba
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 17:17:32 2016 -0700

    added file name functions.

Src/C_BaseLib/NFiles.H
Src/C_BaseLib/NFiles.cpp

commit 1e1c279ba41b75d6670520c73eed09708145760e
Author: Brian Friesen <bfriesen@lbl.gov>
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 01ccfb5f6e122862e84b7ae3b895b792244b9720
Author: Brian Friesen <bfriesen@lbl.gov>
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 d2dee333bfca5fb305da934b21414c4958b4f056
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 27 12:12:27 2016 -0700

    change how default, some cleanup.

Src/C_AMRLib/Amr.cpp

commit cec928c163f4068dbd5d97d90095efb0356e69a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 27 07:07:49 2016 -0700

    fix assertion

Src/C_BaseLib/Geometry.cpp

commit b9fe517c01b7d3ac1b505bf277f4bf32a7c33dce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 22:28:52 2016 -0700

    explicit

Src/C_BaseLib/BoxArray.H

commit 410671d6548f59a3416f387f00cd9625181bb280
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 81174da4ee4ebd157191935e702ea686313cfb9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 16:12:45 2016 -0700

    clean up FB

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d8fe990e75cc477cab54544fea8b3da35211c3b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7faa29464abcf83f7eb3888cd5ec08c8932c242b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 26 10:55:13 2016 -0700

    MemPool: static_assert

Src/C_BaseLib/MemPool.cpp

commit 7194d443830c0ebd30bc247412aa4e9efc6e0b08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 70b965cc94f9d34d3ca63b5aff89b701ee7a994e
Author: vince <vebeckner@lbl.gov>
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 8f0452ded238f97bbc8290e1bd823ea5df20bfc4
Author: Ann Almgren <asalmgren@lbl.gov>
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 da0c58fd96e46323f018924bee9d26d9596698a0
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 14:44:12 2016 -0700

    limit buffer size.

Src/C_BaseLib/FArrayBox.cpp
Src/C_BaseLib/FabConv.cpp

commit 00ae1cea8ef0e8da63b50a0b10a006ea2bf0ae3a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 13:01:32 2016 -0700

    added directory creation tests.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 344873d67119607d14d2c7763da725583850ade4
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 26 12:58:00 2016 -0700

    updated UtilCreateDirectory

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit e4940c16608d30a4c6332d77b43d4264e08912b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:53:54 2016 -0700

    fix tilearray memory profiling counter

Src/F_BaseLib/layout.f90

commit cfa7a5df6990e62117b60abf3039041602bf9103
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:48:56 2016 -0700

    nullify fortran pointer in bl_deallocate

Src/C_BaseLib/mempool_f.f90

commit c6df358858f100f9e326291e10fa51673e49a0b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 25 15:10:33 2016 -0700

    use constexpr

Src/C_BaseLib/MemProfiler.cpp

commit abeddd4f0bba1a1cc845807bec61115cda15d4d4
Merge: 535fe77 dd6181a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dd6181a91059fa84da1981aa906264e157289982
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 535fe779ed3b7999c86272587df7791d086aee41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 24 18:57:48 2016 -0700

    update because BoxArray::define(const BoxArray&) is gone

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 5cc6462d4d3de78a6b43da1e844fddf420415b7d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 87451a8c4bbcc37a30a3d2afb5129348b11e1c65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9dee60b57f9aa99a1a75728a666dd8f3b2a4e1da
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 68e6ac5ee5d4a4f29b6664bd4c019802a920b9ef
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3f209bffcde7a79c76ee2d24b4340800fd7d0000
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 06f36ed02bd163b661710520125efb480e90a787
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a1b55f1ca9863c6a06cdc9d072231599627a4d83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 23 07:33:28 2016 -0700

    make ~FabArrayBase just in case

Src/C_BaseLib/FabArray.H

commit 2b81914948429444d7dc1fc0cddd70bbec03aac6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 22 17:03:04 2016 -0700

    virtualize a few functions in FabArray and make VisMF a class for FabArray<FArrayBox> 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 f93c7c5b6adff62736728fadda3f0ea80f9b8e65
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 22 14:29:40 2016 -0700

    added dir tests.

Tests/MKDir/MKDir.cpp

commit 19a5b243b529a7e00787e307015090aeac2f0eeb
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 16:30:16 2016 -0700

    code cleanup.

Src/C_BaseLib/VisMF.cpp

commit 391256842d2e983c6093a99ebb9410296308917d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b2073cee431dfc5365c52eb2c501de2a0b2fc3f0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 21 14:33:22 2016 -0700

    some code cleanup.

Src/C_BaseLib/FArrayBox.cpp

commit f079dd7a9510632b6ac1979c1928a1741a2cdbd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 38d19b60d981dc71bcbe996b2db4ba3d048369eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 791407d71c5244673cd4a36662507c3ee560b55e
Author: vince <vebeckner@lbl.gov>
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 754d3805f8339bd60e2470dfbd122b468b6a8aa4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 872ef6bab747636c0f4086022edbf5bf57eb101c
Author: vince <vebeckner@lbl.gov>
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 c29b8c337c5d6498874693b8a0783403591df07b
Merge: 147638b 1ddb953
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 21 12:28:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 147638bd64e704f7849da91504bb5d8994cf974e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 1ddb9538b27bf8cfea3d503ed8edb9ec02eaaa64
Author: vince <vebeckner@lbl.gov>
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 3641b641c7196011f3ab87d1a7c990f00d53667d
Merge: ad07114 70304c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 20 19:33:46 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 70304c16a3981a9e591a5ccf4f0576b3f7358008
Merge: cb41d52 19e17f3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 20 12:39:20 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit cb41d52ceee850ecc5de8bc565803f3ef9095e2f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jul 20 12:39:15 2016 -0700

    remove profile call.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 19e17f344373af3e8240b2a6c899793262fd43d4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5fd051b36d3a54a5b0a8510a9799572f75a9f243
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 17 13:07:59 2016 -0400

    detect variable mismatch in comparison

Tools/RegressionTesting/test_report.py

commit 5dd647bca3a37fc4ef84cc07e3435060dd085d1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ad071144c91a3ee41319bede942d8af1822db857
Merge: bb8f42f ade08f7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 14 10:03:17 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ade08f76f051954e2b5d760b82e3402c4d722b00
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9219d56700097259118a92f83fb8747f3adc63b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 13 12:51:32 2016 -0700

    Fortran random: add more static_assert

Src/F_BaseLib/bl_random_c.cpp

commit c848f609182ee19c2d1f349e281acf413075aed9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 12 18:30:01 2016 -0700

    Fortran random: add single precision

Src/F_BaseLib/bl_random_c.cpp

commit e2e6e7a8acad6fb311b80fa45c00f65ec0c0c11b
Merge: bf3cb03 12e9925
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 16:33:44 2016 -0700

    refix name change.

commit 40fb363bfacf7cb09230c1baab6e4e8069033af2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 12e9925c8fda1b8dacab99630ea80ce6536faf88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bf3cb03a84c133e8218824b51f7cfab15e8a69f0
Merge: f9c6762 527bf43
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 16:03:09 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit f9c6762d5d506e9a36bde549eeff056dc5a944a9
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 15:59:38 2016 -0700

    add a default real function.

Src/C_AMRLib/LevelBld.H

commit b03e71d823234e57f74342c831e49e4411f58f85
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 15:41:32 2016 -0700

    dont free the comm from fortran for intransit.

Src/C_BaseLib/BoxLib.cpp

commit be07a5fce321209ff37b33c9f860e201c04de596
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 14:32:32 2016 -0700

    flush another cache for MoveFabs.

Src/C_BaseLib/FabArray.H

commit 690f5e7de6606ecaf5d4026e4c5d28dda06e0c19
Author: vince <vebeckner@lbl.gov>
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 f2c69c59d503e873a116df5e454cff6af1b5fcfd
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 12 14:26:08 2016 -0700

    remove unused vars.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/FillPatchUtil.cpp

commit bb8f42f814920dfbf67b924c17d99b9118ae0f82
Merge: dfae566 527bf43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 12 14:55:37 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit e4f61530162450c2bf33bac8a071fe4cca176438
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 14:07:46 2016 -0700

    merge fix.

Src/C_AMRLib/Amr.cpp

commit 527bf4339b1ec1adbf4405d4d47e54299ee74962
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 09001e549f231bd3e386ab1a3df736fed146f7b0
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 13:33:32 2016 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.cpp

commit fd1cf86046460719aa25d9903f0c68046cf497ad
Merge: 27cc3ce a9b1a1f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 11 12:19:05 2016 -0700

    merge fix.

commit dfae56617be1d861a7ba05ac891de042ff0e9bb9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 11 09:55:21 2016 -0400

    minor formatting

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit 129705b267628c9d4c29fa1ce9aa908d5f750dec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 11 09:48:46 2016 -0400

    replace redefined name

Tools/RegressionTesting/regtest.py

commit 27cc3ce0bb544d3206cd28c0248327017f502e0e
Merge: 3c6085d 418e329
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 16:59:48 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 3c6085da5c23154672923836aef2c08e1e29029a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 16:59:21 2016 -0400

    a little cleaning

Tools/RegressionTesting/test_report.py
Tools/RegressionTesting/test_util.py

commit 418e329ec6dd2be328d3508a768b8f6626316170
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 217cfbb157ae2ff6685483ee0a06b9d91f34f2dd
Merge: c6abf08 409be0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:55:47 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c6abf0818e877886a13dac2866913778aee9ceed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:55:32 2016 -0400

    use is to compare to None

Tools/RegressionTesting/regtest.py

commit 409be0af20ed4ec6a055fc318384ad37c364df0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jul 10 11:51:20 2016 -0400

    actually check whether the user-specified compareFile exists

Tools/RegressionTesting/regtest.py

commit b035c2d88edee2c40b843e27c831de010bf6c08e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 4fd292bad34bb200a4dcd1619d46d5f4c422af39
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 15:08:17 2016 -0400

    explicitly send return codes of success or failure

Tools/Postprocessing/F_Src/fcompare.f90

commit b4faf15d4b5ef4791b40aef334db5281d96a213b
Merge: 91dad08 8176a2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 14:55:58 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 91dad08b67c58639f470bc50891107b615d1d16f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 8176a2f8273f6258872319e88ee45567dff85dd0
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jul 9 14:49:44 2016 -0400

    Write a plotfile on demand with plot_and_continue

Src/C_AMRLib/Amr.cpp

commit e2b8c0d14449bbb4895e0e1afff0e2c4fa118163
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c04e630b991edb129fc2a3a3054f8c642d60fadf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 12:55:31 2016 -0400

    no really, .pyc

.gitignore

commit 60eb0eb4e05bc0cb0f8ab33392b2b19fe5d137e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jul 9 12:55:04 2016 -0400

    add .pyc

.gitignore

commit 19d2d2d6be8205060c5be0e8f2295f04d7768785
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a9b1a1fd429ba1b682749808cf20dd2d025bcb2a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 17:47:36 2016 -0700

    copy more vars for comp resize.

Src/C_AMRLib/Amr.cpp

commit ca7a8a354b0f3a9a5cd953678c487460ecd3807b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7895f237d7ca0254d91d5c368787a4930c709e7a
Author: Marc Day <MSDay@lbl.gov>
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
Src/Python/src/boxlib_wrap_2.cpp
Src/Python/src/boxlib_wrap_3.cpp

commit 9cd5ba0ceb87ce895837581a9cafdfb01a6c9424
Author: Marc Day <MSDay@lbl.gov>
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 5babb03e4c644a95adc7f510e4604c27dabccfae
Merge: f8434f0 b4e253d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 8 18:37:18 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5a79389385ead2442e8aabe0f58bfe5de756cc9a
Author: vince <vebeckner@lbl.gov>
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 741f04332fa9ef6fd2b72de0a01f9a4a874a8b4b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 15:21:12 2016 -0700

    remove test output.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 6b8be66cf6639046197d9c01d71d43f15c5ede04
Author: vince <vebeckner@lbl.gov>
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 b4e253d7c73055dc84dd55d75a9d46a217057bda
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 8 13:31:12 2016 -0700

    added serial initializations.

Src/C_BaseLib/ParallelDescriptor.cpp

commit a6e43ded7fdb40082eece730394ab574277f542a
Merge: cb130b4 2549a2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 8 10:40:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit cb130b48fd0794a3e4eab9bccada7c2ea9c30b2e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 2549a2a99a82cd85f4b0cdf66bca04b65d984d76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 8 07:35:08 2016 -0700

    fix make

Tools/Postprocessing/F_Src/GNUmakefile

commit 02b573211db641d57a71ec25393ed954d49e6567
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 8 07:22:24 2016 -0700

    fixed a typo

Tools/F_mk/GMakedefs.mak

commit d2628c19e51a77bdedd5ea8e7ec3fdf31477ae07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c9f77d4837c0d2723348c7e7752615e16d2499d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4e366d0f957bc425a8988af3e02c2e47412afb30
Merge: 9cf3ab8 df98653
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 22:09:35 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9cf3ab8516b38daf57af32e0e7180b5d30baf471
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f8434f0ce949fc48321c97e946d9131c9073ffc5
Merge: 79b7bb6 df98653
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 18:45:49 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit df98653b2943c35c0cc8c66e1bdb909aac4b2dcd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 16:45:56 2016 -0400

    copy -> move for executable

Tools/RegressionTesting/regtest.py

commit a5d6cbaaf9a78fd954eef54074beb7daf10419be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 6 09:57:45 2016 -0400

    clean-up memory to quiet memory sanitizer

Tools/Postprocessing/F_Src/fcompare.f90

commit 79b7bb674d761ee98309c53c06672af72677417c
Merge: 9149bcb f97b7e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 5 18:48:33 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 9149bcb0efb2aec3a2a906f6ee81121bb5ae3755
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jul 5 18:48:24 2016 -0400

    remove trailing blanks

Tools/RegressionTesting/suite.py

commit f97b7e1144cd6fba5b3b9b1d189c22eb665a5e13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7ecc8c44b63ece879c9161cda6b7bffc6be6947c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 5 07:00:43 2016 -0700

    Release Notes 16.07

ReleaseNotes/release-notes-16.07

commit 4514924e2d1b8608fb45ad625db04017a1b0470c
Merge: 8ee5a13 f4abc0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 5 06:59:44 2016 -0700

    Merge branch 'development'

commit f4abc0a00e2015ee1fcd9d1de4f16510cc0078b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 cc7c213016993c67976db929a38383896e3ad9c1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 4 13:05:02 2016 -0400

    remove legacy comma warning

Tools/Postprocessing/F_Src/fcompare.f90

commit 9cc12191d766e23e389c424bd649e936cc788dc5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jul 4 12:51:25 2016 -0400

    fcompare no longer needs --infile1/2

Tools/RegressionTesting/regtest.py

commit 403f634031529482e97210e718958173187fa3b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eb8c9f9548b03c720477bf0abceda13b1a5b7bc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d3acb0760942281cd2abe04db8f1a9f28459176
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9f09e8ab700bab0b246c4d6d7a3a3f7dc1fbff55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 28 10:51:07 2016 -0700

    indentation

Tutorials/Tiling_Heat_F/advance.f90

commit fb3870861ea7bb02e09c4fa724e2179e7b25b5f2
Merge: fefa60f 7dcfaab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:02:53 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fefa60f3e246b0b0ca30df220c83ec9f5466ca4a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:02:40 2016 -0400

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit 7dcfaab445353c778db672e6f492c2a15fc6327f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 28 14:00:45 2016 -0400

    latest version

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 84d86d626c7d3da5427c6d0f11c4204230edb44e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 19:29:06 2016 -0400

    removed my accidental changes in makefile

Tools/C_mk/Make.mpi

commit 22b8174411713c96eda54c412ab49bdb79dbcbe7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 19:28:10 2016 -0400

    fix typo

Tools/RegressionTesting/suite.py

commit 97b1f3486f48d444221387ebd04fb328a3df128c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bcf032e2558f055b0511b96ab041df151bd3c627
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:46:09 2016 -0400

    remove some debug prints

Tools/F_scripts/write_probin.py

commit 5f15a56f2761cfd0db4235ff001e92ea72372962
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:40:48 2016 -0400

    sanitize apostrophes in the slack

Tools/RegressionTesting/suite.py

commit 120bec97339b97c33eec3d8c257dd11ece0951db
Merge: eaa7492 c197e45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:39:04 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit eaa7492b15dbfc75173371ca339ddfd4a837d945
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 15:38:54 2016 -0400

    add future

Tools/RegressionTesting/suite.py

commit c197e45dca24c2bbcfd8a7205447a000e473b04f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 27 11:24:06 2016 -0700

    missed omp end parallel

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit b2374063cce8bae9bc7125b7e3f706defc512ff0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e6c44ece8580f1c1ceb2455ba4ac3852742394c5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dc9cdec74c6444626188d7724096e1aa99b73bd3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 27 10:01:26 2016 -0400

    using std::isinf for __GNUC__ >= 6

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 5873450c1470c09a0045fd61f1fd7d6fa3fb2ea2
Merge: 49d4182 8a8a88e
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Sun Jun 26 17:10:15 2016 -0700

    Merge branch 'fix_tiled_CC_F_MG_2D' into development

commit 49d4182171d378f31c24b9a91651685eb2d41164
Author: Brian Friesen <bfriesen@lbl.gov>
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 8a8a88e41b44779ca9716025d088e36ed289daad
Author: Brian Friesen <bfriesen@lbl.gov>
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 b68c8867e8dbf3649b36b494440b90e9cd684d60
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 b245a13653d607dbb669c772b36e46ccf3007575
Merge: 32d4568 1f6d4ed
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jun 24 16:47:38 2016 -0700

    Merge branch 'weiqun/random' into development

commit 1f6d4ed5976d2afecf964ca41b7596cdab0d9b9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 24 16:34:26 2016 -0700

    fix pmask in ml_layout

Src/F_BaseLib/ml_layout.f90

commit 32d456897a7ce9ab902d5caa7917448fc813f105
Author: Brian Friesen <bfriesen@lbl.gov>
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 b9d277b72568e89ab1ebd3544d5aebbd369b7d3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c2b841decff7a6f10b83bff483939d581494f9b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 24 13:39:38 2016 -0700

    add initialization flag to IArrayBox.cpp

Src/C_BaseLib/IArrayBox.cpp

commit 18cc38b8b8cecde81e6a792a810d91265d3b8513
Merge: b31035b 926fb7b
Author: Brian Friesen <bfriesen@lbl.gov>
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 b31035be1da1f629df7fcf08e16c8677edb7598a
Merge: 4374e36 59ab377
Author: Brian Friesen <bfriesen@lbl.gov>
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 59ab3778866da96f4d7405b894055d7223c174fe
Author: Brian Friesen <bfriesen@lbl.gov>
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 846b02fefbe7290a316558ea381e2b636ca75af0
Author: Brian Friesen <bfriesen@lbl.gov>
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 4374e364017adb87f2af9604e5980d897130ba39
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Jun 23 21:50:15 2016 -0400

    Add dimension agnostic version of BL_FORT_IFAB_ARG

Src/C_BaseLib/BLFort.H

commit 926fb7bc990bcd4ae10d09fc8a90416e25c5c4f8
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jun 22 17:23:46 2016 -0700

    Tutorials: tile setup_rhs() in MultiGrid_C

Tutorials/MultiGrid_C/main.cpp

commit d36acfda5a603b163ca35b9c2c93e93433d8cdfc
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Jun 22 17:22:40 2016 -0700

    Tutorials: tile setup_coeffs() in MultiGrid_C

Tutorials/MultiGrid_C/main.cpp

commit b23d9e59f6d322f0afe7b2629ad42c2592cde9e4
Author: vince <vebeckner@lbl.gov>
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 a488a98d68924aab2a0a5ee30e05ac051e7a8a57
Merge: f5dd590 37e95a2
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 22 14:15:09 2016 -0700

    fixed merge conflicts.

commit fa3d8baea31cf0d26498deb7ef1451c96b6e39c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c6465e222e2d92952f173d1e3b42f2ccdd010560
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 12:13:13 2016 -0700

    Fortran random: minor cleanup

Src/F_BaseLib/bl_random_c.cpp

commit c0a8defc7ffceaf373a2447a5f7c69c40c42172e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7abddf7d37298faf6eb57bac467a811b61070ffb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 baa46d4d17796e0531adb7d66699c9d01e920900
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 22 06:55:19 2016 -0700

    Fortran random: minor

Src/F_BaseLib/bl_random_c.H

commit 37e95a29d6eeb1d4665e45eaafc833a454e6f96b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a435fe3fca6d4e35a3d0cf35770f9543c00ec8d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 da9e48deb9ed3ed7c980ceb9b138753b69149418
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 37b182fc8930810792d223836723575bd5c22353
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:41:58 2016 -0700

    Fortran random: update tutorial

Tutorials/Random_F/main.f90

commit d16b04eb00aa26dfcd96e29b5b01068193472422
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 21 15:40:05 2016 -0700

    Fortran random: remove change_distribution

Src/F_BaseLib/bl_random_f.f90

commit 7c7de12fbdcb56552d45bd50dd595dae3075fb66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f5dd5900f3ef7df357acde3866f4d75866ef79a3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 21 13:57:18 2016 -0700

    add new test to makefile.

Tutorials/Sidecar_EX1/GNUmakefile
Tutorials/Sidecar_EX1/Make.package

commit 2191b221be40a3ef37bd790e6e4a1c88322c8203
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 16:41:39 2016 -0400

    remove debug print

Tools/F_scripts/write_probin.py

commit 4e398a10efc55cfb9d152c35afa767b1094125c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 16:40:32 2016 -0400

    fix priorities

Tools/F_scripts/write_probin.py

commit 9443bee4516b96b4922112b0300fa74167c5d873
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 21 12:58:44 2016 -0400

    add some help

Tools/F_scripts/findparams.py

commit 17b54f07b401cae511795832f523018d2d982e4c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 20 21:38:46 2016 -0400

    some cleaning -- no change in functionality

Tools/F_scripts/write_probin.py

commit 48fb87de44a91d22a04c0da1c3a10634c1267c3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 20 14:35:44 2016 -0700

    remove extra MultiFabUtil.H and .cpp.

Src/C_BaseLib/Make.package

commit 4d7acd04021e55adc794da5edb2b2aa7a980ca96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4757a4034ddd3e5ecf13997d61a8180e1144afe5
Merge: d201f6e 689256e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 20 18:58:41 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit d201f6e559526858758fb754258c21fff0e60f58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7190908b3efafb87b7705efc66a2c8e8852dee72
Author: vince <vebeckner@lbl.gov>
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 8ee5a13d86237b958a1d628f2cb0929584caaff9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jun 20 14:35:44 2016 -0700

    remove extra MultiFabUtil.H and .cpp.

Src/C_BaseLib/Make.package

commit 689256eb6c29e334e61c7b3573ffd3b6a1ecba94
Merge: b4cbaf0 9eda5cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jun 18 16:20:19 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b4cbaf0d50fb897c90cbc575322cb92a9bd80eaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9eda5ccb971bb93bb4e20aaab13d22c1008af54c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 16 15:15:45 2016 -0700

    GCC option for fsantizer

Tools/F_mk/comps/gfortran.mak

commit abade70376cb162d786bf1c0acf05841c53d47c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 16 15:15:12 2016 -0700

    Fortran BoxLib: respect do_init_fabs parameter

Src/F_BaseLib/fab.f90

commit cfb9bf2c9b7a06efbb7dfe19e262f5d1c20ccbee
Author: vince <vebeckner@lbl.gov>
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 19b8225790254794bac7c664e37186b533c47d40
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 16 12:29:19 2016 -0700

    random sidecar ranks test.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 8fa4fa123c6dbebe5747188a7605f440f03802a4
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 16 12:26:56 2016 -0700

    clarified comments.

Src/C_BaseLib/Utility.H

commit 98edfa89a1b6f12b8257379de0b7483939a83941
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d80c690f213f7c4132d2efa113dbd3727b003340
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 59e5ba24226f20284320c2f68120e7ee537c3530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 559a50951cc1129ca1c0beb87bed1c11b195c8f0
Merge: f6c347a 4e6ea8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 15 10:37:30 2016 -0400

    Merge branch 'master' into development

commit f6c347a0f900633d4c0dadae3a4f6e5f4d950ddb
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 a452aa09ec9c6dff7fba87e08ea6182f0316e9bf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 15:18:00 2016 -0700

    seed verbosity

Src/F_BaseLib/bl_random_f.f90

commit 83cc3c8d5274c2ab2143a6d1b5582178bba0549c
Merge: 41b0361 37969e1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 14:04:49 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 41b03612d7a1f800892df31482bd44937f1be0aa
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 14:04:32 2016 -0700

    print out the random seed info

Src/F_BaseLib/bl_random_f.f90

commit 37969e1976e377cd685379975d61ee130955792e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 13 13:07:26 2016 -0700

    Fix spelling in comment.

Tutorials/PIC_C/solve_with_f90.cpp

commit 4e6ea8d7c959ae3403989f2de92e9c0dff12a54e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 b2d7284a668e34e6db6772020ac0d8bac75554f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a7dd8bdf1275c123e4d169018ce94acd29a183d2
Merge: 0f537fc 34c1b2d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 10:37:16 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 0f537fc9e060692b758dce629bf88dbea4d455f0
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 13 10:35:56 2016 -0700

    mpi settings for laptop

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 34c1b2dcf5faaf40c18059b0504cab383d1438b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5e15da676569bfda06e0c052772b234163662b16
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 13 09:13:30 2016 -0400

    add integrator

Tools/F_scripts/makebuildinfo.py

commit 3bcd8d17a93873b020f1f49670c03f99377d80e7
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Jun 11 23:35:19 2016 -0400

    Add Cray compiler version variables to C_mk

Tools/C_mk/Make.Linux

commit 560db9f4dfacff7684a2d864a8d353d187ad3690
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jun 11 16:45:43 2016 -0400

    the stub version of parallel_tag needs reset

Src/F_BaseLib/parallel_stubs.f90

commit e4a2bd665a5fe05c58741611af56e829e3511875
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 ded4c690c693239dde5bcc6e38da1979aa457ca8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f301a06f6c8265ca16b6a0b605879722159f4d8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:21:13 2016 -0700

    new mpi location for naphta.

Tools/C_mk/Make.mpi

commit 50b868ce8d63643144061a481d064dff787cda49
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:19:07 2016 -0700

    more testing of multiple sidecars.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 0b6f697443c3d294b85fcf14454a648a8fb5babe
Author: vince <vebeckner@lbl.gov>
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 6a9475b8799c2fe67a64799b3d1cc33fc617ff49
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 12:11:46 2016 -0700

    more documentation.

Docs/Readme.sidecars

commit fe38fa861a7704aac4bf427cc1e43ceebda8572b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 10 11:39:25 2016 -0700

    add copyInter support for multiple sidecars.

Src/C_BaseLib/FabArray.H

commit f68f1c1fbd5700d574556dd7437f7aacac5ea66f
Merge: 8eee587 7cd7f83
Author: Brian Friesen <bfriesen@lbl.gov>
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 7cd7f838b9847b761a30b6221ab873954635c78d
Author: Brian Friesen <bfriesen@lbl.gov>
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 35abc24efabf2dd6080b65aad1d7064fffff915c
Author: Brian Friesen <bfriesen@lbl.gov>
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 663544fe49b12de18edf6cbd3e315b87f74e4134
Author: Brian Friesen <bfriesen@lbl.gov>
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 985ebc21f4439ddef113f7b1cba8259dc1485e0a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 16:34:01 2016 -0700

    update for multiple sidecars.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 98b178191b4315352484c9c1a020c462c99f6fba
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jun 9 16:33:34 2016 -0700

    update for multiple sidecars.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit b6346fab1ddbf2c9898388dceb99bf7c6cdd8d0d
Author: vince <vebeckner@lbl.gov>
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 7289dd1872d386074890786ba42408c0069cc896
Author: vince <vebeckner@lbl.gov>
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 8eee587a5572803c1d7e75815b92e2f8ed56003c
Merge: fe60abf 58a0323
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jun 9 18:13:14 2016 -0400

    Merge upsteam 'development' into Adam's local 'development'

commit fe60abf9c1ca2086411d4d7d17486d4041ad4d91
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
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 2f3e12605ef05b4cc5aa00d6fa24401674c4d0fa
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 8 13:44:37 2016 -0700

    include both local and global ranks in filename.

Src/C_BaseLib/BLBackTrace.cpp

commit 4b917b687afe85e7db80c193337f6efeaa758c74
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 7 16:47:54 2016 -0700

    started documenting the sidecars.

Docs/Readme.sidecars

commit 58a032346fb39b2b3050d7a71e937b92b21384f6
Author: Ann Almgren <asalmgren@lbl.gov>
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 96947fba4f8af4cccd14371cd5b5ebc0791cc73b
Merge: b751105 be8d7f0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 7 15:08:43 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b751105debdca92cf0970946aeeb79ef3b2694f0
Author: Ann Almgren <asalmgren@lbl.gov>
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 be8d7f09056dbf34b5a097194340098d151bcb3e
Merge: bb64b23 b2d24ed
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 7 14:24:29 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit bb64b23f6dc318ec6801502f7db20482bf387547
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 b2d24ed1234b253650f0d0787457e8d8b705d920
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3a71ba4e02e474fbb24eb54e21c96e7b4ad60cc3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d8f7b826be6ac749db8b96c01641b91b398685b5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 6 17:04:24 2016 -0700

    write proc number to abort message.

Src/C_BaseLib/BoxLib.cpp

commit 644491f3906157e9c4c670e9498f97aabd4e3e7d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 6 15:33:51 2016 -0700

    write proc number to abort message.

Src/C_BaseLib/BoxLib.cpp

commit c07e7970d30d8450c4a33744518273a19d7311b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 4 13:34:06 2016 -0700

    Release Notes 16.06

ReleaseNotes/release-notes-16.06

commit 16d972d92ab93c47c1f99f7080f5e73cfaf867f8
Merge: 9eae5b8 792ac5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 4 12:54:54 2016 -0700

    Merge branch 'development'
    
    Conflicts:
    	Tools/C_mk/Make.defs

commit 792ac5a743d56ef1bde43f986fd02bd71ff783d7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 47807e4362f5278cf6e74963a5187bfa31b5f646
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f0c49d9ed238f1f4bee145238225ffd4dbb683ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jun 3 16:26:37 2016 -0700

    define intel versions so they appear in job_info

Tools/C_mk/Make.defs

commit 6071394e5c38010ebbd84f6ae2f6a804e645dfb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bb89a7db6e511af645abf839767508668946c1aa
Author: Ann Almgren <asalmgren@lbl.gov>
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 6c1a2affcdf5b833986bdd274a46b78193fa0169
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 2 09:50:58 2016 -0700

    Make: option to use fsanitizer for debug build too

Tools/C_mk/Make.defs

commit 6c3e0ae1a4499690236dce7d8d1d9c20555577f1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 22:39:35 2016 -0400

    some cleaning

Tools/RegressionTesting/test_report.py

commit 6c85d0328509dd60a1eb7583b5edf055d15d4983
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 22:39:27 2016 -0400

    simplify run()

Tools/RegressionTesting/test_util.py

commit 636cfc416a7783a3d7d3a6d7196c6b2d390ad663
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9814217b870627372f947134c8fa2e2205325360
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jun 1 20:33:31 2016 -0400

    a little more clean-up

Tools/RegressionTesting/regtest.py

commit e2de7dc31e58da8bc2a85088770de85e7793e729
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 01c69f1c4e10b92ca742f631fa938965078c6dd4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3592a09826ca6eb4ae6b3121eb303fa0bf71e4d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 39a617f655407d50222068a48a42215ba3b7b4ac
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ece381eee676e2ec6d7101f1d8323af388eb69d6
Merge: 553d30a 193faaa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 31 12:29:41 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 193faaa5718e34544314af476031b02e604ed3d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 20:44:45 2016 -0700

    MultiColor_C: minor

Tutorials/MultiColor_C/main.cpp

commit e89d789f12d1bb95d361d4ed07d13601cca50d07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 18:10:12 2016 -0700

    MultiColor_C test: add a ne fortran file

Tutorials/MultiColor_C/ff.f90

commit 8fffa7cc39596d202b168429b8c96ad8656654ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eb26240969ef7faa20ec11cbc96a0605961eb7a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31d37bf289996d2b060dce121b06a26ca57a35e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 13:38:31 2016 -0700

    color BndryData

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp

commit 49cae39bed3e512eb6dd0d276c279812863a2b06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 30 13:28:44 2016 -0700

    color BndryRegister

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit 7af662492946bdabfe7983e64664817b015e07c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 553d30a6d46533ed43192dfaa3598e5e3f4b93a3
Merge: 78729fc 151f8a6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 29 22:28:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 151f8a688e5a1734c9f058e97ffff05cf7c98113
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sun May 29 22:17:06 2016 -0400

    Turn off PGI Fortran debug symbols if using OpenACC

Tools/C_mk/Make.Linux

commit 75376b97bcf9de8d08d1956b7fc4b7d5ab0cd396
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ebbae08e1b6672699dcd94b22153cbe59dd0c7cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f761d17d5f1926e6d98f3c5459d75ebc76977e19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun May 29 09:47:45 2016 -0700

    Fortran bl_random: assert seed >0

Src/F_BaseLib/bl_random_f.f90

commit f10c67208fee9457298f72227d1e8b5e0c0f7df1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5a4e91df3809c121a0ffd3a7d5bd0b7fe9fc050b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 21:58:06 2016 -0400

    fix formatting of the job_info summary fields

Tools/RegressionTesting/testnew.py

commit a6a1d7faae3ec8c60d7fbf856d95deb124d77793
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 21:11:07 2016 -0400

    if we produce backtraces, we fail

Tools/RegressionTesting/testnew.py

commit 78729fc72a6f3f08b1af65181d5c1112118cae3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 20:32:17 2016 -0400

    shorten some headings

Tools/RegressionTesting/testnew.py

commit 074e2aa8f98e2ab9b72b98a0c38e49f3816731a8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 18:58:19 2016 -0400

    initialize the job_info fields

Tools/RegressionTesting/testnew.py

commit da05ade716a65033f06865749b11b7a48424c6b6
Merge: c14401d 8f24082
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 16:02:43 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c14401dae0457a6a08c6b21eeec9847402011dbd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 16:02:22 2016 -0400

    cleaning + copy job_info to web output

Tools/RegressionTesting/testnew.py

commit 8f24082ee7c52885ffa61fbfa5895558c0824eb6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:56:34 2016 -0400

    update prototypes

Tools/C_scripts/buildInfo.H

commit 0ff28f2d3e1cf18e164043e986f4d5f53353b636
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3d7c62be7b05ef563c1ff95b7019a736720d5a9c
Merge: 872630a 9137641
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 14:27:26 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 872630aa97c010d1bb3486cca03591f2d08af8e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 913764148efc5397428375159959629f4d70be27
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat May 28 13:43:59 2016 -0400

    robustify the summary table

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit 88194d2adddf64b9ca5e29b428fd999b11a80783
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 21:46:51 2016 -0700

    Fortran bl_random: minor tweak

Src/F_BaseLib/bl_random_c.cpp

commit 85e68cc646a38590013a8748622b6d206c880b26
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 21:41:27 2016 -0400

    updated test file

Tools/RegressionTesting/Castro-SBU-tests.ini

commit b180eb1b00169bfcafacc09ad67a27586345fa12
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 caf0f1e09c5eae47627f6c5b3cdb9ce574052d73
Merge: 23e3ef1 ad40f8d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 27 20:03:20 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 23e3ef1669f08e8138a30eb7bb7de0e3ddd5aed7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ad40f8dd422f62de74e37e35893162edabd8e5b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d3401ebb590540d3988a6ac6efffc049a41228f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 be9419da58987b7648572d9753a74f62bb61cff8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d9af67e5e1d59810cbba312ccdc60ff5134a845
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 27 15:40:52 2016 -0700

    forgot to add a file

Src/F_BaseLib/bl_random_c.H

commit fe6de64532abd4fc6511efbf35e1e15401e5b90c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ab0efd2d68af799350e3c922ed99a888dffd615a
Author: vince <vebeckner@lbl.gov>
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 e5e1ad5453a640b6eae2435c890b809404b6989b
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 17:30:15 2016 -0700

    fix for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 8ac9b2a4d3b1177cda20a21a4affc25443f33be9
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 17:29:17 2016 -0700

    added more error checking.

Src/C_BaseLib/ParallelDescriptor.H

commit 17384985b9ab5b6709ec57516337a4f8d78446e0
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 26 14:48:05 2016 -0700

    added function for which sidecar.

Src/C_BaseLib/ParallelDescriptor.H

commit db3841078cd371b02ed296d1f475e154a3b66a50
Merge: efc17f1 c4d2b9f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 26 12:07:07 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit efc17f1dd8fff0d68005cd2e50cbee0ff7c4e4f0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 26 12:06:52 2016 -0400

    make this work with python3

Tools/C_scripts/makebuildinfo_C.py

commit c4d2b9f5b725074b594961957b67b5c5a46c4c80
Author: Max Katz <maxpkatz@gmail.com>
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 92af45bfc5c7f7b6e093c52ca38b236af16b7493
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 25 13:20:16 2016 -0700

    free extra groups.

Src/C_BaseLib/ParallelDescriptor.cpp

commit c5f1b27b6f70f8802e2ee2bb53014974e56b61dc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 bd44b0de658e9a5df55a6d8c454a12fac548b16d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 2fe5efbe48f60d7dc032cb1fdbca9f7693770cf1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 12:45:36 2016 -0400

    sync up with the version in C_scripts

Tools/F_scripts/moddep.pl

commit 9df4fb965d4101e0b9bb2f9cb779fd573a4e203e
Author: Max Katz <maxpkatz@gmail.com>
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 da74b7ea04080600471540bdb5a4363ecfe52e97
Merge: 919cba8 f964d7f
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 25 11:42:37 2016 -0400

    Merge branch 'development' into openacc

commit f964d7f3c91e2978971438f501568d6e66c17309
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 40ad46de290097bdfff17711b15c39a87deb6188
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 11:15:28 2016 -0400

    make the Fortran dependency script recognize .F90 too

Tools/F_scripts/moddep.pl

commit 9a40a1c8e8708f05328ad1a61c4ae03acaac8cf9
Merge: 34997c4 e493450
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 10:40:59 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 34997c4000a1ab3de36e233ed1f5da7f83d2ce1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e49345048292994ff938401202c16aee2b86262e
Merge: 318ca6c bb9f3d6
Author: Ann Almgren <asalmgren@lbl.gov>
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 318ca6c4f0d4c1dbfbb0086bab55554990ee4da7
Author: Ann Almgren <asalmgren@lbl.gov>
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 bb9f3d64ae442584bbbf40f228a36e5b1e6cc343
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 25 08:40:46 2016 -0400

    fix the OMP here

Src/F_BaseLib/ml_nd_restriction.f90

commit 0a24a157b0cdb6cc3aba8429692e0cda79abbc5c
Merge: fa8895e a4fe94c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 20:42:45 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fa8895e98e6e4286f22af501e2439f9333eb84e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 20:42:22 2016 -0400

    cause why not ... define FIVE12TH and FIVE32ND

Src/F_BaseLib/bl_constants.f90

commit 92fa8c51ca3dd45594715976ac214e114e3b6531
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:13:07 2016 -0700

    added a new test.

Tutorials/Sidecar_EX1/NSidecarsTest.cpp

commit 039bf2ddde3564ae6ee04c7254823e70fcb3aa42
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:12:47 2016 -0700

    added a new test.

Tutorials/Sidecar_EX1/Make.package

commit 65dd12525c634880287bd4b8f139a971de0cde7d
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:12:23 2016 -0700

    update test for latest boxlib dsc.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit c7617c38143d74241edf1d1d0939e344ef61347d
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 16:11:37 2016 -0700

    fix group free for zero sidecars.

Src/C_BaseLib/ParallelDescriptor.cpp

commit a4fe94c7f9c04b07fbec3837676059a0ec97e56e
Merge: 2fa5f51 e12b358
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 24 15:26:30 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2fa5f517d2fb45fc3adb17d03b103f57a7e2057c
Author: Ann Almgren <asalmgren@lbl.gov>
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 351b0af891d32df3e1666435b8b0f7c4dd9b8f20
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 14:21:35 2016 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.cpp

commit a0b0e7e102b99ae1e3a685e6f3a9f0a5a5476a19
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 14:11:18 2016 -0700

    default arg.

Src/C_BaseLib/ParallelDescriptor.H

commit d2da9753995d23ac87c6d09d6bd008ba3d1d979e
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:58:30 2016 -0700

    fix for zero sidecars.

Src/C_BaseLib/ParallelDescriptor.H

commit 4613779b2300a28813af60384f40bcec1f7418d1
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:45:15 2016 -0700

    additions for multiple sidecars.  fortran interface needs testing.

Src/F_BaseLib/parallel.f90

commit 9ac403a22f6620e1a1a4e47cb127ffb57e3e53ce
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 24 13:44:17 2016 -0700

    additions for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit e12b35845ccae8564da3cc339bb5625169325d04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:35:45 2016 -0400

    fix convert_type wrapper for None

Tools/RegressionTesting/testnew.py

commit 54ab7e3579d64638e2db229abbc30eb3ec7de8ea
Merge: e830c38 37ee0b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:32:10 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit e830c381ac737800afa745c4134799ca93027905
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 14:31:58 2016 -0400

    a little clean-up

Tools/RegressionTesting/testnew.py

commit 37ee0b85cde6dc58f61cc6be19eb09e32a85a2e4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 24 11:01:42 2016 -0400

    gracefully handle the "grids don't match" error from fcompare

Tools/RegressionTesting/testnew.py

commit 9ad353b5872e5d549b02ccad02a65023464b548a
Merge: da9ad0a 1d75688
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 22 16:39:23 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 1d756884e0779f0f0a89816adf1086415fb66cfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b52641ab4b1aa8e5cb1bb8e3216d277e4134bc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 83822b4885744c493fa818940caebcd2885263cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c9d4a74c7e45109f61670519deaecf734f17e59a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 107ac44f0b6b4e24bea6ee2f1d5871a37c3aca87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 21:52:18 2016 -0700

    operator<< for ParallelDescriptor::Color

Src/C_BaseLib/ParallelDescriptor.H

commit a76aec166d7fe1b143e757312be9b68a1dc83f24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 71ee01ddcf0e928d6b7a7bdfc361145ad3a1daf1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 055648c85867b3207ba9f5fdae0d23b55d8b1d0c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1e80e20024d2e776eedb55a177aabe5a2f6018b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 71b8711fe3b5364c7e2d77aba463cf7d9f566281
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b3706b953b927f05c1cba96ff72c40963092738b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 20 17:01:19 2016 -0700

    clean up an unused template for parallel reduce

Src/C_BaseLib/ParallelDescriptor.H

commit 9eae5b88c2cf97d8c8ea250c36710d6ced7afd58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 136b6392c23d41a256662424af2291840c8a75e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4e0234d8cf2fd8b1488aef527a5dbb97a299284b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 63b78366a82eb9d88d406c24fb3076aa75c257f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 20d3b1c2ac184406d1bee40686459dca7f2eac58
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu May 19 19:51:30 2016 -0400

    Permit disabling of PGI OpenACC

Tools/C_mk/Make.Linux

commit 54a361ccf5f1947ff565053321bc26a519435c61
Author: vince <vebeckner@lbl.gov>
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 77f06c16733d282d30f63de4fe994cb39039bb87
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 19 14:56:56 2016 -0700

    fixes for multiple sidecars.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 1c2bb06731cfde122545e4f54985ad5d2389b968
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 19 08:24:11 2016 -0700

    fix bug in my last commit

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 4738dbd8059c31ed823e97e63cc1fe0ed0d9f5d5
Author: vince <vebeckner@lbl.gov>
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 d6016415ffc8b1edc181b9019a354a60f3f4bd62
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 18 16:03:46 2016 -0700

    update NProcsSidecar for multiple sidecars.

Src/C_BaseLib/ParallelDescriptor.H

commit 0919756abd7aeb173be7f89750a04ae430c213d5
Author: vince <vebeckner@lbl.gov>
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 66abf3925b6f321dca66721ff0053386b3235422
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31152ff89df765c6aa37da6a400ac5bb61e0b4d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 17 12:25:10 2016 -0700

    typo

Src/C_BaseLib/ParallelDescriptor.H

commit 9b928b6f129a8b38b192d9add29fd4ae21e6c6c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 17 12:19:02 2016 -0700

    runtime parameter team.reduce

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 9e48c86442eeab6b16d6e3925e1be1241d5b334e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 51769c0228b3b80b73b386fb9b79d9de38190000
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3e42ba77dd2bb585d879789f18563c4cbd3becd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c751987811c6e6c764ad155f2025037c0dac68bf
Author: vince <vebeckner@lbl.gov>
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 ac427b36f9dbc3df641d581f0e9d4e7e0792c8ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ecfc8baaaef7af3cbf9d01c9b860c11d4d0bc546
Author: vince <vebeckner@lbl.gov>
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 c9261e6de550bea45105c07389ba41f48552f549
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 12 12:14:32 2016 -0700

    removed cout.

Src/C_AMRLib/Amr.cpp

commit da9ad0a75d1fb9c3adcd1f131af8e198c5490c92
Merge: 31acd25 5d7efcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 11 22:24:33 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 5d7efcc2e7f127301836e6545d800aa74b050a4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e18e3d925fe707af27ece62ca4b8ae9edf9accf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e32e8b18e077979a698598529d9165cfcff272a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 241026e928590ff7b125b5d6aae51568f1e18d6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e18c71de2c95e555d40da181a0eb6f4fcb17ba5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 10 15:57:53 2016 -0700

    FillPeriodicBoundary: avoid writing to valid regions

Src/C_BaseLib/Geometry.cpp

commit 76e16df2b2c997ef89e08a6450a7861c0e0318e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 35f6d847e796354c00f542731612b521af7e531e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 919cba8e4374a7f8c555e387b66c34af1aeaf698
Merge: aaec651 58152be
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon May 9 18:35:11 2016 -0400

    Merge branch 'development' into openacc

commit 1a2f8ec82893f5e828be07af6307f3b9649be37b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 9 14:07:19 2016 -0700

    baragon makefile

Tools/C_mk/Make.defs

commit 58152be5a2829bb12d46df1db9ed82a91702a427
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun May 8 18:55:09 2016 -0400

    some more OpenACC PGI flags

Tools/C_mk/Make.Linux

commit e59fd253b98ecdac88183cce335159119c1a1810
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 17:33:24 2016 -0700

    update make for baragon

Tools/C_mk/Make.defs

commit 3424a54597b6c631a378c266cff2f30852852cfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 07:15:33 2016 -0700

    fix some minor data race

Src/C_BaseLib/MemPool.cpp

commit 35085648eeb2974356664680b3c4c3d311b3da03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat May 7 07:06:00 2016 -0700

    add MultiFab::Saxpy

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 5becf0db126f163652088f85036c443e4808b7a2
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 15:29:09 2016 -0700

    dont abort on CheckFAPointers.

Src/C_AMRLib/Amr.cpp

commit 4da0c7dee0b06e65529cad2bb86be445f111065f
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 15:17:28 2016 -0700

    added option to not abort on errors in CheckFAPointers.

Src/C_BaseLib/FabArray.H

commit 734537a203be2d7b147265594bf842aebfdb03a3
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 13:36:17 2016 -0700

    cleanup diagnostics.

Src/C_BaseLib/FabArray.H

commit 85662263af5fb7dec8ec69c593f12eb569d38798
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 6 13:35:21 2016 -0700

    add call to fabarray internal check.

Src/C_AMRLib/Amr.cpp

commit d3127163e453cd76ce90d4ade9ebcbf9afa86242
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1c84b25282f08643d2630adb46a3c2b7d22564ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 87d628da1e32293ad8f0e6588a4e2df36eb5020e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f13cd54b34c9ab0b6175f7b14836ef547f1f3d20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 66640b59c2d2dd2e3204e99f034141ed848629b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 17:07:26 2016 -0700

    fix logic in new BoxArray::complement

Src/C_BaseLib/BoxArray.cpp

commit 7deed4faeccfcce72f78410e78517b7af0e959c8
Merge: dfa74ae a40ef15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 14:38:37 2016 -0700

    Merge branch 'development' into weiqun/complement

commit a40ef15f4ea61aa253ab2e1a04d91f12a99dff8c
Merge: 17bb255 4cc1c90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 14:01:39 2016 -0700

    Merge branch 'new_reflux' into development

commit 4cc1c906d492973ad680689e069c65de7beecae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 5 13:23:54 2016 -0700

    clean up

Src/C_AMRLib/FluxRegister.cpp

commit 17bb255f7a1d409000ba7e3db14db57515925dab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e8f6f98304a02caa24ad49c5223e6d4080baa3f4
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 5 12:35:30 2016 -0700

    another check for data integrity.

Src/C_BaseLib/FabArray.H

commit dfa74ae94a3515c3b398da0b94c86d92910c2333
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d1d520efc3439d0cae7ecebb201e0d76149bd552
Author: Max Katz <maxpkatz@gmail.com>
Date:   Thu May 5 01:57:54 2016 -0400

    Update the probin script to handle OpenACC declarations

Tools/F_scripts/write_probin.py

commit e5c66c35d8d327daebba9c57fbe0f4cb06b3d815
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 18:12:50 2016 -0700

    fix some errors in last commit

Src/C_AMRLib/FLUXREG_3D.F

commit 6b7813ccf8a2c03495371f391a26e26603be46f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a5763f202f2a3d4088fa472a353afb10a0e5b46b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 15:15:42 2016 -0700

    omp in FluxRegister

Src/C_AMRLib/FluxRegister.cpp

commit f589cf83ee151635ef633940fb261f4905627166
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 13:53:26 2016 -0700

    omp in BndryRegister

Src/C_BoundaryLib/BndryRegister.cpp

commit 4f6e12c26d469d7f0a9338e8bda3f5fc63768f88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 12:46:34 2016 -0700

    comment

Src/C_BoundaryLib/FabSet.cpp

commit 181dea331ebd02b02c941e51edf3a973717a9fe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 12:19:44 2016 -0700

    Switch FillCoarsePatch to using the new FillPatch

Src/C_AMRLib/AmrLevel.cpp

commit 3741ecda0b1f71df81121145d2fbb248ed89afa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 4 11:24:08 2016 -0700

    fix the new FillCoarsePatch

Src/C_AMRLib/AmrLevel.cpp

commit 193226ca3f2bc9e6cfe783cd9b4f926a4b0f2b8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5b250a5cba99b30e752ac47cd1f256ad2bc699cf
Author: Max Katz <maxpkatz@gmail.com>
Date:   Wed May 4 12:50:44 2016 -0400

    Use pgcc for compiling C code with PGI

Tools/C_mk/Make.Linux

commit b304b4fabb15b01b962343288df9c37a835c9628
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 69b535d83127905d0ffa9197d8284fb12a4401c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ddf04fdcc155046cdeb1e4c9b79d81576972c08c
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 3 12:20:56 2016 -0700

    mpi_require.

Src/C_BaseLib/FabArray.H

commit 4a9c25f9ce82bab611411ee81b589162414695cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 12:06:22 2016 -0700

    FillPatchCache: fix a bug

Src/C_BaseLib/FabArray.cpp

commit 0145b2eec0492bbae46b983b4ae8a0ca8f13f482
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9e36dbf507db4f14c3bbd5b5b23e8c6d6aed02b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 3 08:29:36 2016 -0700

    FillPatchCache: fix some bugs

Src/C_AMRLib/FillPatchUtil.cpp
Src/C_BaseLib/FabArray.cpp

commit 7a3d673793f1315acc6a9a3112142e1a0900d75e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31acd25d37b21d589af0c05a070f4ec779972048
Merge: 596058a a84a678
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 2 19:15:30 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 610e92f3aab83731b86cc2d7b0164823d4591841
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a84a67892b840672df50948a16b3b7c71c7c6264
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 10:40:50 2016 -0700

    Release Notes 16.05

ReleaseNotes/release-notes-16.05

commit def3694b8a604baf871fae548c93a95da2032a6e
Merge: 3465a64 4b6f471
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 2 10:13:10 2016 -0700

    Merge branch 'master' into development

commit 3465a64aaacf3402334c13d52c5498ccc9d56388
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3f6fb05661d46fcc8b9dc7bf6f5b62b1d16bdae0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 18:34:44 2016 -0700

    fix leastuseteam forUSE_MPI=FALSE

Src/C_BaseLib/DistributionMapping.cpp

commit 47ac1a30c7750d3b7721465a1a302039d39d9026
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e972938c3b825e2fd96c353e50492f4a0b045884
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9634cb9540e37a3fb0c059c14a528b53c8cb8af2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 277643662200ac6a4f03db5035a1293a1cc3dec8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:09:27 2016 -0700

    const refs.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c4e245bbb3b7895c6d671a056b402c02dfdacb22
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:08:36 2016 -0700

    const refs.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 63be2dedf5dc81fc7ce8e61015949218c00b19f3
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:08:07 2016 -0700

    const refs.

Src/C_BaseLib/FabArray.H

commit 2ec45eba50cc82d7eb990867955c31b53b251237
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 29 15:07:17 2016 -0700

    delete dm cache.

Src/C_AMRLib/Amr.cpp

commit de76c103ebd3879ff8091588c86c76795cf2ed72
Merge: 847fb4b 21bb807
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:35:59 2016 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 21bb8079a7896fd2bcef086dff600ce691e11474
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:05:30 2016 -0700

    Profiling reduce

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2b30c77674c09f9c1801d100f9456a8dc7582788
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 29 10:03:50 2016 -0700

    TinyProfiler: setfill

Src/C_BaseLib/TinyProfiler.cpp

commit 9ca1f8c5c02a33738bdcdb591236f3f8a8221cbf
Author: Brian Friesen <bfriesen@lbl.gov>
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 aaec6519aaa247d186b1d950944ef7f38188eba6
Merge: 47b0f0d 2279193
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Apr 26 15:26:44 2016 -0400

    Merge branch 'development' into openacc

commit 47b0f0db049bd4351c380a6e4f2164672fc2f059
Merge: 2dda63c d2c6007
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Apr 26 15:26:32 2016 -0400

    Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc

commit 596058ab707270b200f923ed8c185304374c8a7f
Merge: 1425351 2279193
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 25 18:05:08 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 54911462d36fe813928c3f59bda4ad43d337e9e9
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 25 12:59:25 2016 -0700

    delete distmap cache function.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 847fb4b99f393e32ee2d469296a03dc946bfda23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 22791937872a4f118880ae6860e0922204474700
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d5938db13cf3ce99f170b1197c1887e83d8f52a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/FillPatchUtil.H
Src/C_BaseLib/FillPatchUtil.cpp
Src/C_BaseLib/Make.package

commit adb9772bd706610cada9cfdbb3e151b4c88f5978
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 11:01:26 2016 -0700

    Revert "move Interpolator from AMRLib to BaseLib"
    
    This reverts commit 9509a39a1528ee2eab21f9e589991620fed6df5a.

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/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 c022149e9e0a76cbc03c95537cd6f27a37df70f8
Merge: 4da1a83 28607cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 25 10:23:26 2016 -0700

    Merge branch 'development' into fp2
    
    Conflicts:
    	Src/C_BaseLib/Geometry.H

commit 28607cb97ea7eba5823e58a8b4a9d81475d452ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b25271747309766600fd91481cbb1e5ef5c1a04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ee86b997e22bc87d778fd0bf96e4b392a913f02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6aab1039758a0454535938e9276284cd564577a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5a6ccea3b1482a6b42cabf0da55db7b4f3295b0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 45b32da0521e503d962f9210c1d03de388a8fa63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 deba0673798f04d693b8e6253bd5cc5ad266233e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b3a270c075237c63098a2fc06666300d783de003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a8d0a623633497c2ea8bcfffa0abd779b29bfab0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 960e1b0e30117172612dee5282e60e1050351d41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fdb464130c25b82ea2692c45c349e5db31111246
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 14253514a46ef239775e6c760f74bca780b3a2b0
Merge: e6a31c1 be1769b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Apr 23 17:47:54 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 1a22a81235423f5e3b17b738845f084644a1541b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a89de2352662910e09e354e62a0b17e945b5e5de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 be1769b175620e1ef866fac5f58a85f5e713e0e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4da1a83af75cc5037f0fbf76e4f566171d30ef63
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Apr 22 14:44:33 2016 -0700

    minor changes in profiling

Src/C_AMRLib/AmrLevel.cpp

commit 9c03cdf0a9ecd83c34b1367b2b845dfabc96368d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d59190e4def29bce9d3c8f44f4c912dc0a6d4afc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5b14f09350a5efc97fa6ce5a6d1c420ae967c2cc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a8727c270ce8f36532d7f283f648d11fbf12bea5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 22:29:38 2016 -0700

    more general periodic copy

Src/C_BaseLib/Box.H
Src/C_BaseLib/Geometry.H

commit a58ea375de7e45038ad4bc8cf64b10b98ee28156
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 17:57:36 2016 -0700

    BoxArray: need to update type after constructing from boxlist

Src/C_BaseLib/BoxArray.cpp

commit 4e1a640b10a6dbeb431615b4029fa5cf14aa7c4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 21:41:31 2016 -0700

    fillpatch: clean up

Src/C_BaseLib/FillPatchUtil.cpp

commit df2bc7abf2624dc15400a44c9dd5c7801f145042
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 21:36:45 2016 -0700

    periodic copy: bug fix

Src/C_BaseLib/Geometry.H

commit feaa017604dced8f5f3ef9e89c11b60815deb490
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 17:57:36 2016 -0700

    BoxArray: need to update type after constructing from boxlist

Src/C_BaseLib/BoxArray.cpp

commit 73e74ba26fc10c37fcfa058f034cce62a937b07b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:45:05 2016 -0700

    new periodic copy: remove empty boxes from list

Src/C_BaseLib/Geometry.H

commit d7312a10d447dc88248191510ffe3e81dde7f3d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:39:44 2016 -0700

    profiling two levels fillpatch

Src/C_BaseLib/FillPatchUtil.cpp

commit 75a38e96ae6d7696a0744572e6fdb3a642ca1a44
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 16:39:07 2016 -0700

    fix the new periodic copy

Src/C_BaseLib/Geometry.H

commit f0eb04de19238a8594bcc0926a194624cb272e55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Apr 21 13:36:29 2016 -0700

    change default blocking factor from 2 to 8

Src/C_AMRLib/Amr.cpp

commit 3980d2c765ec0daa36420830becac7daaabd7b64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fde3ced840c905f2ace2626e8568c5a43f2e1c49
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:11:04 2016 -0700

    cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit af1d1fbe784dfcfd4c954e3fd26f7c67f6789617
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:08:35 2016 -0700

    redistribute particles when resizing sidecars.

Src/C_AMRLib/Amr.cpp

commit 031aad31c9c044c75dbd3ad3388661970d7a0f27
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 20 18:07:44 2016 -0700

    syncronize sequence numbers across groups.

Src/C_BaseLib/FabArray.H

commit 9509a39a1528ee2eab21f9e589991620fed6df5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 14:17:21 2016 -0700

    move Interpolator from AMRLib to BaseLib

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/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 85f11ff41dab48e1522db742581db585989ccdeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 11:14:33 2016 -0700

    single level fillpatch: parallel copy ghost cells too

Src/C_BaseLib/FillPatchUtil.cpp

commit 9bcc951219df1c29f6c04366befd529d8ee795d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7db82ca58ba6d495478f3bc30eaab8c6db444011
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 20 10:43:45 2016 -0700

    derive: fix box type and ghost

Src/C_AMRLib/AmrLevel.cpp

commit 70c13f81870a1f2cd70a494be3d42fb7ff346107
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 110859c0049d4eeb5ed8eaf38284485f59c42cdc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 15:38:29 2016 -0700

    new fillpatch: omp

Src/C_AMRLib/StateData.cpp

commit a4020dea4b70989622d6b76ace5185a3bdf0fee1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 19 15:37:46 2016 -0700

    new fillpatch: linear interp in time for level 0

Src/C_BaseLib/FillPatchUtil.cpp

commit 424a49b77bcec30711a0a3bf6831ab8f2f59df1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2bdab79ac39a08487fa9d754a1d2218872e2648c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77b8e8e87494334b1fb354beebb159ad30b4d443
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 18 14:56:50 2016 -0700

    TinyProfiler: avg % --> max %

Src/C_BaseLib/TinyProfiler.cpp

commit 0adfdcc50bed5a29133a2e81a4a56dd36ff5b5f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 18 14:53:35 2016 -0700

    TinyProfiler: avoid finalizing twice

Src/C_BaseLib/TinyProfiler.cpp

commit f593822bcc066185ad848049c3e20cca9e50f3f6
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 18 11:12:30 2016 -0700

    remove diagnostic.

Src/C_BaseLib/FabArray.H

commit e6a31c16f1242f246ff43e2b2cc07e0ef4f8eefd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Apr 16 21:35:30 2016 -0400

    make this python3-aware

Tools/F_scripts/findparams.py

commit 4b800f1fbe6e95d47ddd7ce4f462d1d1a41f165f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 15 18:11:59 2016 -0700

    resolve Fab_noallocate fabarrays for MoveAllFabs.

Src/C_BaseLib/FabArray.H

commit ac38ccb212451e1f74b4bf6ec8bf336929f2045d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 15 12:08:12 2016 -0700

    removed reduction.

Src/C_BaseLib/FabArray.H

commit 8ea1e562a26e6d1cba328d2b2c43bbc81ee03a82
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 16:04:26 2016 -0700

    fix for nyx.

Src/C_AMRLib/Amr.cpp

commit e202a26214deba76a6a4dd4415312ae110c4bbac
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 15:07:06 2016 -0700

    remove temporary diagnostics.

Src/C_BaseLib/FabArray.H

commit cc619f8fde66cf72450789a066e04ad560e7c008
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 14:25:24 2016 -0700

    implemented BroadcastBoundaryPointList.

Src/C_AMRLib/Amr.cpp

commit a144b72e9a90c5b6f9e0c3fc7a3d9dd659aa5567
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 14 14:23:46 2016 -0700

    implemented BroadcastBoundaryPointList.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 1f3b3956e035424e622c843d04a8522b002d9aef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 17:38:33 2016 -0700

    TinyProfiler: fixed pop

Src/C_BaseLib/TinyProfiler.cpp

commit fabbacd9af508dbdffa7e2b36ea14beca1055b05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 13 17:15:57 2016 -0700

    TinyProfiler: fix OMP

Src/C_BaseLib/TinyProfiler.cpp

commit 586507c985cc30a5282590fe899888088ebda43e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8dda631ef552f17247d41107be04905191bb078c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 54eed4580da28e0ad4c2fb448a0217c3a29f19c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2be16aa1ee8ed785d158459c8991e457773f0be7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 13 12:57:25 2016 -0700

    remove diagnostic.

Src/C_BaseLib/Geometry.cpp

commit e9d6e11b7b27fe3e4210fce4ca5e9c73f835c3ff
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Apr 13 12:12:32 2016 -0700

    C_scripts: squash warning about "hdf5" module

Tools/C_scripts/moddep.pl

commit dc3c7afd3fa50269678d2af21720482361b32297
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Wed Apr 13 10:37:00 2016 -0700

    C_scripts: squash warning about "iso_fortran_env" module

Tools/C_scripts/moddep.pl

commit 546196aba38fe93e324977783afb0762cf8dbfe0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 12 14:37:52 2016 -0700

    update comments

Src/C_AMRLib/Interpolater.cpp

commit 87fbe270999a7e4c8395e1eb5d70cffa613e333f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:56:45 2016 -0700

    remove unused variable

Src/C_AMRLib/AmrLevel.cpp

commit 01864cdec38a8261beaa25f8e7a9331f2e957130
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:55:23 2016 -0700

    FillBoundary: timer

Src/C_BaseLib/FabArray.H

commit f2fe6298fa3f3d78738744592e321e030a1333b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:53:15 2016 -0700

    add fixediter option to MultiGrid_C tutorial

Tutorials/MultiGrid_C/main.cpp

commit cff95a5132ed5602e6738edfeefcc22f1e8da11b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 17:46:50 2016 -0700

    comment out the mpi-3 fix recommended by NERSC

Tools/C_mk/Make.Linux

commit b8e64b9bd4d4d31b912d6feb88c07f3cbc44d6c5
Merge: 8f158ad 75789d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 16:29:10 2016 -0700

    Merge branch 'development' into pgas
    
    Conflicts:
    	Tools/C_mk/Make.defs

commit 4b6f47113ec4f0d4327a0db2d1a55b0764e873e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 15:42:12 2016 -0700

    release-notes-16.04

ReleaseNotes/release-notes-16.04

commit 75243ee1e44764ecae14b701be0d3fc78ff7e8d4
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 11 15:33:26 2016 -0700

    fixes for nyx.

Src/C_AMRLib/Amr.cpp

commit 75789d19e9f3e429f9d2a9f89de7d0f0fe8a78d3
Merge: 41aa4bc 9cb379a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 11 14:38:33 2016 -0700

    Merge branch 'master' into development

commit 1b6b13b8a1af6e56f070d88d5031d097708ef3e0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 8 13:49:50 2016 -0700

    clean up proximity maps.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 1dab77ec3e0959794a844680f2eb24f58e3c3c50
Author: vince <vebeckner@lbl.gov>
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 89b907eae1e10c17de8e8eb039147f0844c3d02a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:45:39 2016 -0700

    stubs for dynamic sidecars support.

Src/F_BaseLib/parallel_stubs.f90

commit 522c333b6eebdab67c9362dc2195eafe7fc9853c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:06:57 2016 -0700

    fix for non-mpi.

Src/C_BaseLib/BoxArray.cpp

commit ef06aae08aa11ac7e2d70dae46df2c33dbeb111f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 16:04:27 2016 -0700

    fix for non-mpi.

Src/C_BaseLib/FabArray.H

commit a4cc93dab0b82c8d84c8b9c75b49c33e53a01649
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 6 14:38:54 2016 -0700

    remove old SidecarProcess.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 41aa4bca90fe3a85bfdad602bdb1af441409eb90
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 dbbb7c7a3e0e1d2e602e0c5f8933c998dd6132ab
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 fbf65dd6143a1cf148babb973c67ff3ed3c1b597
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ac820f7ffb98205f945dcdf7da5b474a1f138dcf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 14:45:51 2016 -0700

    get dx for plotfile write correct

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 55c9e5dbd20445924fe6a275791a4069de44d430
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 14:08:27 2016 -0700

    updates from Aleks - add coarsening factor input

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 8db0b5ddbc85da0dbdd482f0bf21fad6960c2c44
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 13:22:24 2016 -0700

    turn back on 3d coarsening of plotfiles

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 71773f92f2a9012c8e280fc9202a7f2d148e6734
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 5 13:19:18 2016 -0700

    add fcompiler option to f2py

Tools/Py_util/GNUmakefile

commit 7abae19a66e06ce80ddf26f01f416f2b8dbe5be5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:58:33 2016 -0700

    revert accidental commit

Tools/C_util/Convergence/GNUmakefile

commit 99050b8885aae6e49e3cff64d30ed5c4656d8737
Merge: 2da8856 905452e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:57:14 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 2da885699ca5934a8c2230eea9f3ab673397a5a1
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:57:00 2016 -0700

    forgot to add file

Tools/Postprocessing/F_Src/fcoarsen.f90

commit 905452e97c9163b76414c75707d585ddb56fad42
Merge: 652dc2b 023b6a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 5 12:39:25 2016 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 652dc2b991dc7d1c3175681ff9f9a228524943c1
Author: Ann Almgren <asalmgren@lbl.gov>
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 023b6a5bb7bb272cec811b14998014085145f0c3
Merge: 94d7869 685bef8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 5 12:23:21 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 94d7869a2aedf59f598e727db955f04c755bc64f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 fc2437922a5fb4ca37368c105242c051db2be52c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 4 17:21:51 2016 -0700

    check return of getcwd.

Src/C_BaseLib/BoxLib.cpp

commit 685bef8b2224ef64da30a18e4c2129bd203f3397
Author: Ann Almgren <asalmgren@lbl.gov>
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 8535890dfda0dc51545e602385f5a93ca6a3538d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 4 12:05:19 2016 -0700

    fix for particles.

Src/C_AMRLib/AmrLevel.cpp

commit d3f5141be3a8768bbf1d540f4172bdbd716970b1
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 1 23:00:33 2016 -0700

    Use gnu99 instead of c99 if using GNU compilers

Tools/C_mk/Make.defs

commit c6391d28c4adc8c6ef2831bdd80f4a90d7e17f91
Author: Marc Day <MSDay@lbl.gov>
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 d2c6007d04b0c5bdd9ccb790d6d748174b579e5d
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 7001c76b206c5f1852d8df3ae0805749593f880e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 31 17:35:27 2016 -0700

    fix for copyInter sidecar tutorial.

Src/C_BaseLib/FabArray.H

commit 24fef5b614f1458fbbec0a4c58ff91fb4dfe0adf
Merge: 93c1f55 5300714
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 31 17:06:29 2016 -0700

    merge with master.

commit 17d1d78cd395ca5747ce4bff8a986fe160b93d78
Author: Ann Almgren <asalmgren@lbl.gov>
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 d5cb69fb1c508d2ff658aa7d99e31f23060c0eab
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 31 14:45:01 2016 -0700

    Fix some oops from previous commit.

Src/F_BaseLib/create_umac_grown.f90

commit a736625a3f3d91b8dd042238d22dd78ec12252e9
Author: Ann Almgren <asalmgren@lbl.gov>
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 9cb379a599ffde00f31b72159443e3da050e3268
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b9931eeacb93d6fe0c356704e53b106344998a01
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b250e7b4b21d3c679f2eb29058ce75a2c9e00c3
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 9c5cb6d5a8cc57143c33176c7372b901db2fd860
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 7e0805f15ffc6ed249b3be7cd54a1c70810f0951
Merge: d733336 913dbca
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:31:00 2016 -0400

    Merge branch 'development' into openacc

commit d7333366289d9f0d5bb30ae2acc9acfaae36220f
Merge: 6855367 8a71467
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:30:04 2016 -0400

    Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc

commit 68553674d47538bc1ee6b9364e1f79f353f05996
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 30 15:29:52 2016 -0400

    fix indent

Tools/F_mk/comps/Linux_cray.mak

commit 8f158ad1f15d843fde3c09952863268099f96196
Merge: 7e8fbef bfceb35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 30 09:12:45 2016 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit bfceb352f3d255d031996eb4d81f368360b2f543
Merge: 1ef0b9c 913dbca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 29 12:56:00 2016 -0700

    Merge branch 'development' into pgas

commit 1ef0b9c0d1811d3381691add34cf8e2744197309
Merge: 2df7cd5 5300714
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 29 12:55:29 2016 -0700

    Merge branch 'development' into pgas

commit 913dbca1eb564e4df03c3e3a4e749c82a90157fc
Author: Regression Tester <ccse.lbl@gmail.com>
Date:   Tue Mar 29 11:02:48 2016 -0700

    regression test: option to use valgrind, --with_valgrind

Tools/RegressionTesting/testnew.py

commit 0fcfe104fbc498329ea62652203a053c26792b3e
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Tue Mar 29 10:56:24 2016 -0700

    battra F_mk

Tools/F_mk/GMakeMPI.mak

commit 176c6944269951a8d7d72e174a42713269251124
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
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 580ab8eaab1ddc6e470b467d1b06b7ac30c045f5
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
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 b8c7cb04d2d0cabf156b0483986a5935f92edb5b
Author: Marc Day <MSDay@lbl.gov>
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 4de76c131324fd13112caf70b284b6aae2eb668d
Merge: b8781e4 8bae1b5
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 28 14:06:18 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b8781e487220f4afc8670459710392aa2dced48a
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 28 14:06:12 2016 -0400

    Add 5/6 to bl_constants

Src/F_BaseLib/bl_constants.f90

commit 8bae1b5c81a41668622cc5d82b4641949c0ab2bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7e8fbefbd65cb978fec1e85b8577458f5df9e52b
Merge: 2df7cd5 5300714
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 25 14:48:08 2016 -0700

    Merge branch 'development' into pgas

commit 93c1f550d9fc1e6e2ed75a576e599559571e04d6
Merge: bf6c4bf af19914
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:46:05 2016 -0700

    Merge branch 'master' into dynamicsidecars

commit bf6c4bf1275f67dd8aad89b465400598a6faa0db
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:40:27 2016 -0700

    premerge cleanup.

Src/C_BaseLib/FabArray.cpp

commit e2e16eee1a52feba2270d0c6dff2e8a07fed92c2
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:38:23 2016 -0700

    added more profiling.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e29f781d02d968726c3777105b428fed8549d6e7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 25 12:37:53 2016 -0700

    premerge cleanup.

Src/C_AMRLib/Amr.cpp

commit 2df7cd5df0ad3e19cd291aadfa9e4386a9f7b929
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 24 15:59:15 2016 -0700

    PGAS_SMC: should use NTeams()

MiniApps/PGAS_SMC/SMC_init.cpp

commit 3decbf1a5adf70f14fbd63ba76ed36669037013e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 24 15:52:24 2016 -0700

    PGAS_SMC: change defaults

MiniApps/PGAS_SMC/SMC.cpp

commit 9371b9858b2bc02f108c386e6c96424b37c0bf66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 be2917755b3d89beda1920d91ef760698799bf05
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 22 11:56:38 2016 -0700

    add periodic to output.

Src/C_BaseLib/Geometry.cpp

commit 5300714260c2cf994feb69e9b84bf4180cb64794
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 22 07:48:26 2016 -0400

    fix typo

Tools/RegressionTesting/testnew.py

commit 2a36ac4e0c77278a0e523557b1efcae0b0b34c9c
Author: Brian Friesen <bfriesen@lbl.gov>
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 db6e18e2616e7e2cce01126497352686ed75fd1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 21 13:14:35 2016 -0700

    update make for baragon

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit d1211141f4b3dd8f99a9dd8f3c814666b8d0f809
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 21 13:14:08 2016 -0700

    free MPI_group

Src/C_BaseLib/ParallelDescriptor.cpp

commit 783b35f6eef435236595d304f651156460ed02cf
Merge: 32a0bfa a461a3a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Mar 21 10:54:13 2016 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 32a0bfa63658b9ccef1d31f22c5a5248f1827f3d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Mar 21 10:53:58 2016 -0400

    some slack cleaning

Tools/RegressionTesting/testnew.py

commit 18a216b48e01436f486b42c8aedb924ea0dc656e
Merge: d745ca5 a461a3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 18 14:23:51 2016 -0700

    Merge branch 'development' into pgas

commit d745ca5215dc221d745c9166780766b0a5305b11
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 02ee7a655fe9e7534fcb987f2a1fa6faf0126771
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 18 13:10:51 2016 -0700

    code cleanup.

Src/C_AMRLib/Particles.H

commit a461a3adea2d321a7d94d315efcbdd76335526c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77867387f094f87c1a8c07a87e559108cbf2178d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:52:52 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit 8224e6160a7a889126414532de49861d2576e84b
Author: Emmanuel Motheau <emotheau@lbl.gov>
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 a74852e808c85425c21d6712cdb4c49eb967c52d
Author: Emmanuel Motheau <emotheau@lbl.gov>
Date:   Thu Mar 17 16:50:21 2016 -0700

    Add varan machine

Tools/F_mk/GMakeMPI.mak

commit 91a37c09f022c462322b25432414f13b21e89f41
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:48:09 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit 62b2b697043416e5b58f91f98351b40f039daf33
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 17 16:47:17 2016 -0700

    added profiling, cleanup.

Src/C_AMRLib/Particles.H

commit f8271bd0c6aad1e72992e8901ebc8cd83151bb48
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31fdae155b05786c40584df889b70e62890eefc1
Merge: f911ccf ce604a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1075b6babb32227ca5bbb3fabc0ab5688926f7f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ce604a709b0e22e8c5ba6d4332ecee9b44191892
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1a2493eae27511b7cef5d3cc9e6741de53f2f5f7
Merge: d4e3fd6 313036a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 17 10:22:44 2016 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 313036acf21ab10ab7a97a2abd6a744a44cb516d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a73971e26f5a6d1569de679bab1eeb0bcfa133e3
Author: Marc Day <MSDay@lbl.gov>
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 d4e3fd68a6af1ce4789b0ce0a3e7d7c723ec2a17
Author: Marc Day <MSDay@lbl.gov>
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 14d8aaeeb6ee0438adf246cc69ebfff4c52d7873
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 16 13:08:17 2016 -0700

    add section for start/stop.

Docs/Readme.profiling

commit 7619216e724b2f67f89b1125142feab54ed39f4f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 16 12:23:36 2016 -0700

    fort profiling fixes.

Src/LinearSolvers/F_MG/mg.f90

commit 8a47149ddfac3ef3d0d5419ee1166a529cae484f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 71cad31f93a1d13e213dcddb28143526f3d4b868
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 16 10:35:15 2016 -0700

    MemProfiler: add VmSize

Src/C_BaseLib/MemProfiler.cpp

commit f911ccf9ebf60da75ea3fed043436a8816021274
Author: yzheng <yzheng@lbl.gov>
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 e96f52f897e4b7c3696dbf3becbc030f5ce48972
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 22:02:50 2016 -0700

    reduce max # of copyassoc to 25

Src/F_BaseLib/layout.f90

commit 7287156dd4e3ff77d1431449c5ac81cf1ff568ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 22:01:21 2016 -0700

    MemProfiler: fix an index

Src/C_BaseLib/MemProfiler.cpp

commit 4e2918fb89549126ddb59fbb6cb1a247bbff7d2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 21:13:00 2016 -0700

    decrement copyassoc_cnt

Src/F_BaseLib/layout.f90

commit 893acb4acebd04f9c79b1e8a107bd23d62b831fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 20:40:15 2016 -0700

    cleanup

Src/F_BaseLib/memprof.f90

commit 38b6b4aa9ee0e1e7f28d887e7aca78249d84d5a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 18:13:12 2016 -0700

    MemProfiler: add data form /proc/pid/status

Src/C_BaseLib/MemProfiler.cpp

commit 047914c771885a87e50373ea7ee4bfaf380423e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 17:07:22 2016 -0700

    add a header that Intel complains about missing

Src/C_BaseLib/MemProfiler.cpp

commit 2e4ee9ee69766ec9fd4e4cf63d6e6d55b813c25e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 66bcb57f7897a82d2ec669d5634e60e4e9ceb2dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8fdca51d2262cd2d5a80ebe23cf45745883db0b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 16:05:47 2016 -0700

    layout: add more memory counters

Src/F_BaseLib/layout.f90

commit c6b8354033d518b183535ebe64901bd7dcf26a39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e12c41b2803916854cbd647c34ee012b8812fdcb
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 15 14:26:00 2016 -0700

    use max_level for size.

Src/C_AMRLib/Amr.cpp

commit 60929a9297033250471c1da292d739e11a03d25a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 13:28:44 2016 -0700

    remove gcc-2

Tools/C_mk/Make.defs

commit 35eed5356f710a3556633b8b941396e227437cb2
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 15 12:25:05 2016 -0700

    some cleanup.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit e890d91072e50518935cd0699fd77fb4aecb99ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4a47765b8791438a39eb3a3242bb9c746d1e1b8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 12:17:06 2016 -0700

    cleanup

Src/F_BaseLib/layout.f90

commit 52d8f8b10e358fd33acd4ba18da20addb5ecf0c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 15 10:13:35 2016 -0700

    Fortran copyassoc: change the max # allowed

Src/F_BaseLib/layout.f90

commit 2a9dc240fb824ffd6f4c0b26547e89b324a2c274
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 14 18:36:56 2016 -0700

    added test to copy from sidecars to comp.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit e844e235cafb920d2a5812f168f50f12082a95b1
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 14 18:34:03 2016 -0700

    allow copy from sidecars to comp.

Src/C_BaseLib/FabArray.H

commit 44e5744d9ed3a3728259f68c1198f96557c9cff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 18:32:18 2016 -0700

    MemProfiler: minor mistake

Src/F_BaseLib/layout.f90

commit ff53ab84eefc3d3a3feb07bd40411f4374148718
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e5dacdec3608462a016982056a66ab1d37286e3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:50:00 2016 -0700

    MemProfiler: skip print if high water mark is zero

Src/C_BaseLib/MemProfiler.cpp

commit e4ffb3bf6059e09547600bebf02239ddf9e74225
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f5b0c967438768cb4132073e728bef745a4a4866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f8d93fde4bee5cffadc8dd757086dfb6f446289
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 17:27:38 2016 -0700

    MemProfiler: sort the output

Src/C_BaseLib/MemProfiler.cpp

commit 0dc72ceb66ca3ffbe7918d7cb9c3938ab0f829ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 15:59:23 2016 -0700

    MemProfile: add cached memory

Src/C_BaseLib/MemProfiler.cpp

commit 8a2aec44fe014a0360d59fc168828b8e4c105a1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df5142b258e4367fb19d495e44e38d2dbf102c84
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fcdc25b5cbdc44041ab11d7b82f9c03a379bb066
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 14 10:36:19 2016 -0700

    fix a new bug in BoxArray I introduced yesterday

Src/C_BaseLib/BoxArray.cpp

commit 64b01d991e85f9140cabb269f560d2154fa3f969
Author: Brian Friesen <bfriesen@lbl.gov>
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 b1a7068bea831064597046885bf67b4bae6257f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 20:55:18 2016 -0700

    MemProfiler: fix BoxArray::removeOverlap

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 1752b8cab8d21126e354edbccc498a563e3465e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 16:58:51 2016 -0700

    MemProfiler: optimization

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 9a8a9f8f4b4e071012be6b82a1c7b891cf917c46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b004dfde7a38c86f6fc38f624da058e181b57a51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Mar 13 12:58:45 2016 -0700

    MemProfiler: pretty

Src/C_BaseLib/MemProfiler.cpp

commit 0973e69e20b854a3c5a12920f7d6aa169a922e1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c345b66ec823ecdf3f0336f46919dabc120ef83e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3153ab32a9825ccbcbef7dac751c7b56515fc815
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 22:52:58 2016 -0800

    MemProfile: TileArrayCache

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit b8f6ea6a7bfe68c2dd70b3a8c4d8527e732ba92d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 21:37:13 2016 -0800

    MemProfiler: Geometry

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit f44bd45ceae4b6035dc6d66c79f9cc2af4f80e36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8db73be4dda0bac795fae24afef17ece2d0ca8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5572286aae77aa6b66a65209cf32ecc65b5e17bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7d2889c8f45fb414aaac642e41617a18f455af16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9f0f3e51590661aa5509c3ede436cc1cd27a23fa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 11:09:28 2016 -0800

    MemProfiler: minor

Src/C_BaseLib/MemProfiler.cpp

commit 75e19745dbdc7a81c4a6ad58983ac0f54782b64e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Mar 12 11:08:52 2016 -0800

    MemProfiler: bytesOf function for std::vector and Array

Src/C_BaseLib/MemProfiler.H

commit a26cad180aedc8f506839cabb3955733a602f144
Author: yzheng <yzheng@lbl.gov>
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 7ddaf82cae99ba7bcbce1351352a445e1c9c87a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3b84aa58d2caa381da2ab31b66d11582fc8fe1b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0a36db7bb64aeb98a0dcf6aae293f04c64f36554
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4de2b2dfe6aaa5b87886e3585972c8ea9b331896
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Mar 11 19:44:40 2016 -0500

    latest inputs file -- this has the slack integration

Tools/RegressionTesting/Maestro-tests.ini

commit 47140662befa1af1765e7ef62b817c8bd2a22339
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 15:55:05 2016 -0800

    changed inputs.

Tutorials/Sidecar_EX1/inputs_sc

commit d3c5ec0651ceeb2d90d750d8f9b4b471425c84b6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 15:54:16 2016 -0800

    added several tests for shifted and grown multifab copies.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit edf8e108ef4ab0d37ebc9df5b95c9d2efcc31be1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 671a69ddcdf7cf932d768d89ddd7ad50e68c28b7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 14:34:56 2016 -0800

    reenable assertions, add more error checking.

Src/C_BaseLib/FabArray.H

commit ec8dc20978445ed08a3b52b4445e7ffc71f06786
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 11 13:57:42 2016 -0800

    remove unused variables.

Src/C_BaseLib/Geometry.cpp

commit 7b0540e75ca5f3d0bcf623eefb719393f8bdc09d
Author: vince <vebeckner@lbl.gov>
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 f1087aba21727100f94ac101943a0c0e18629242
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Mar 10 22:04:18 2016 -0500

    fix formatting when variables are not present

Tools/RegressionTesting/testnew.py

commit 1359de9bdd811a99997066dced5cbf71586dcf6b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 10 18:37:33 2016 -0800

    testing the new FabArray::copyInter.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 229ea80abce03805ecb7a12a44064bed7d0e07e9
Author: vince <vebeckner@lbl.gov>
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 b8e8b003ffbdcd4c4f03f21ed7696d864dceca26
Merge: 5f14ba2 a98d77b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 10 18:13:09 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 5f14ba27d00e966cf28534353e91372eedd03a35
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 6f1f7f7d8accb797d59406fa1da57909b30c3e1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 14:05:46 2016 -0800

    buildTileArray: fix reordering

Src/C_BaseLib/FabArray.cpp

commit e7cc029885a4b42f353dc3d4d83b7d1e3ae0512c
Merge: 25a9fd7 a98d77b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 10:58:32 2016 -0800

    Merge branch 'development' into pgas

commit a98d77bebc49cc784c9e5a98163b1bb54772c0a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 10 10:58:12 2016 -0800

    FillBoundary: remove empty messages in case of cross=true

Src/C_BaseLib/FabArray.cpp

commit d708778fc449eb0218a17dcf0d1d39d93eb9b5ff
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 9 18:30:20 2016 -0800

    sync translated dist maps to all procs.

Tutorials/Sidecar_EX1/DestMFTest.cpp

commit 25a9fd7637ebaf61d65724c1db087d463f868b54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2cb470bf13c5265cbabd8b85298ecb4c7fa3d701
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 16:15:04 2016 -0800

    add headers

Src/C_BaseLib/FabArray.cpp

commit 2d8380cd43a88e32b1f8cd0e4499d00eb9e75fd1
Merge: d5f0a66 2b9c304
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 16:06:31 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit d5f0a66e876c06dbc00b24993fbc569b3d3815bf
Author: Ann Almgren <asalmgren@lbl.gov>
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 de63f0bc54f3d9b4296e799ba3e54154ed3b7572
Merge: 8ac8ab4 4e60f2c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 9 15:44:49 2016 -0800

    resolve confilicts.

commit 63d1797aa5367bf2b5fdb296a22e7f837dd84f87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8ac8ab42292d4e8429cc6362aba3357d9f67f506
Author: vince <vebeckner@lbl.gov>
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 4e60f2cd6d8fa547a5c945d29d1d835eac7b4fa1
Author: Brian Friesen <bfriesen@lbl.gov>
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 c63c9d844f4179c862352ab625533ff27a00f393
Author: Brian Friesen <bfriesen@lbl.gov>
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 50204f23178719ca7c2efe8e40381426ab948616
Author: Brian Friesen <bfriesen@lbl.gov>
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 aac2f6866fddd78bee9493f55d9bbcd2ba4acab4
Merge: 9603024 2b9c304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 14:05:38 2016 -0800

    Merge branch 'development' into pgas

commit 2b9c3040df93f9a85f032c6a779d4700a93360c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f3d1c7015c09763d17b188389fde464e6d073581
Author: Brian Friesen <bfriesen@lbl.gov>
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 6b1730f98a8ddc25bb789c97871cf156e7fe3839
Author: Brian Friesen <bfriesen@lbl.gov>
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 54cd30ce51af9803a9c6479d0988c2c45ce4f621
Author: Ann Almgren <asalmgren@lbl.gov>
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 960302433aea00bedc31f9956a0044ae820f7ccf
Merge: 78ccbe5 8430ae8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 11:29:10 2016 -0800

    Merge branch 'development' into pgas

commit fe7c1d7e449e8c07341de89941e73ef2aa605d30
Author: Brian Friesen <bfriesen@lbl.gov>
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 8430ae8c80cc6476faaa047cccbea4338e7a7562
Merge: 519a283 13f77ed
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Mar 9 11:21:19 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 13f77ede1bc81451fb811a2e96e20d620b849c77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 519a283a255c09faba126fe8e803117c11d34891
Author: Ann Almgren <asalmgren@lbl.gov>
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 b71c650cca5e9f1fbd2fd69b598321163e8556ad
Author: Ann Almgren <asalmgren@lbl.gov>
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 78ccbe5292b0f78b3a0b1470f6d4dc2658958649
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 9 09:43:48 2016 -0800

    minor

Src/C_BaseLib/Box.H
Src/C_BaseLib/FabArray.H

commit 4bdb45f9e07fa27176cdb8f0cbd15c4e3d4408f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2ec4dca7511a8519d12017510b4c9148b086f348
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 11:24:01 2016 -0800

    fix typo

Src/C_BaseLib/BLPgas.cpp
Tools/C_mk/Make.Linux

commit d09a445dbe26bf6994aa6513148d9c7669897c14
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 72b1898f3f335033a17093e6a161eb0a08291e3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Mar 8 08:36:37 2016 -0800

    BLPgas::alloc: proctect against zero or negative size

Src/C_BaseLib/BLPgas.cpp

commit 201e60d03f0a89f2ef10f4a6ac35bb6d9749c8ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 7 18:11:28 2016 -0800

    0 --> nullptr

Src/C_BaseLib/FabArray.H

commit 4cecaa4d8da25d38b3665fe87a72cbf0ce4e1b29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6e2a235fa3195194eb2a2b8215a5c78d05ea474c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dc0432184d7834bcbdcf1678407c2ce10e8caf05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a1d3177f552be7487d2ac58cd11afc36ea0acd40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 699e2254e53cc7040147ee5da19f4aff28f32dda
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 8a0e4e43be7b7b94517982ead6e713173076f5b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ee3aae76d25aa1f51daf09b1525170335d6de8a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:20:53 2016 -0800

    Cray supports C++11 now.

Tools/C_mk/Make.Linux

commit 9ca1ec93c3f73cc6c4cba94a9fab48ab68d82419
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:20:53 2016 -0800

    Cray supports C++11 now.

Tools/C_mk/Make.Linux

commit 8665b3d86b156e0cf351a199bb1ae1468449ecb4
Merge: bdab9d5 9e9a20d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 17:09:05 2016 -0800

    Merge branch 'development' into pgas

commit 9e9a20d364be88efc55ab681e38e09569da44b0b
Author: Brian Friesen <bfriesen@lbl.gov>
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 873e2a81aa90e0571f1262d0ffc98259adf8c3db
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 4 16:16:38 2016 -0800

    use new broadcast functions.

Src/C_AMRLib/Amr.cpp

commit bdab9d515a97750c74b4b2ee4bb691bdce23b741
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Mar 4 16:09:00 2016 -0800

    fix LAZY for team

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit fe85b570c5f6fa6af52a97e7cf7f5fce64039ee6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 4 16:03:09 2016 -0800

    move some code.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 16bbb18c3f9f517c97f942637ddae03f5214751d
Author: Brian Friesen <bfriesen@lbl.gov>
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 5f781a82026f041fdc8e46b621217d1909d5635c
Merge: 3bccd76 ad5b4c3
Author: Brian Friesen <bfriesen@lbl.gov>
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 ad5b4c3c0f47184bf6c14fba9caa3baa6e982384
Author: Brian Friesen <bfriesen@lbl.gov>
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 cd6cf78e44706deb821bc4b61570237d68a12a08
Author: Brian Friesen <bfriesen@lbl.gov>
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 4c2d1102ec3f9aa4ca7a3c4c3dff274168d24ca0
Author: Brian Friesen <bfriesen@lbl.gov>
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 c14c39f5a14a22ceda014d4dec1a8df829f2fbc5
Author: Brian Friesen <bfriesen@lbl.gov>
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 217fe6c35de2cea8af382485dfcba80b2e2ea285
Author: Brian Friesen <bfriesen@lbl.gov>
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 359296db185f3dadc5f649eb815cf47c2247d3dc
Merge: c8d2440 3bccd76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 3 17:31:49 2016 -0800

    Merge branch 'development' into pgas

commit 3bccd760d7c027b9ce7533d08fd8c549dc314c9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d0feb307cdc4f65353a8eaf3f025821579ba14bf
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 3 14:03:32 2016 -0800

    fix for starting with zero sidecar procs.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 3aa5246ca743340eb8168ec922a65c7476b782a0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 17:20:57 2016 -0800

    allow nSidecarProcs == 0

Src/C_BaseLib/ParallelDescriptor.cpp

commit f3e28b9d9c05bd20a6b890940ee0b02e35ba917a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 16:58:43 2016 -0800

    allow nSidecarProcs == 0

Src/C_AMRLib/Amr.cpp

commit 6838257d9b2cdcbad872670dd9aa6f0c6b3cdad1
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 14:27:09 2016 -0800

    some cleanup.

Src/C_AMRLib/Amr.cpp

commit 04966105735e6f097023ddcb7e3df3d9787e74bc
Author: vince <vebeckner@lbl.gov>
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 0deca343416e7d8fc255778ff7ef0d5f85082323
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 14:10:55 2016 -0800

    some cleanup.

Src/C_AMRLib/AmrLevel.cpp

commit c8d24409a4a1c82fe4ebb504ec515cb5fcdae5ad
Merge: 3f4f6d0 56ee22a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:40:29 2016 -0800

    Merge branch 'development' into pgas

commit 56ee22a75f6ebdd4831c1a4595138f931341c9a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:39:49 2016 -0800

    explicitly add noinline attribute for gcc

Src/C_BaseLib/FabArray.cpp

commit 3f4f6d0d9815e7172560d7a4c9ad9cbc26a9bc33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:39:49 2016 -0800

    explicitly add noinline attribute for gcc

Src/C_BaseLib/FabArray.cpp

commit 07ac173a75e86a8570f465c94e581b592032ce97
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 2 13:39:18 2016 -0800

    reinitialize fortran data for new procs.

Src/C_AMRLib/Amr.cpp

commit 95ea9ecc4c1834b9302048780b4779a1bee90126
Merge: d57c8e3 41ab627
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d57c8e32b5b5c5c59c58c25909ab94e33be461ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 2 13:19:45 2016 -0800

    minor

Src/C_BaseLib/FabArray.H

commit 41ab627d23b3c741cb93a41443759a20e34a83dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e9c2fdb787909e5147400fd75940d9bbcd7d05a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bb9023cd6bd434cdf1b8b73602448c099152e548
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 de4bbcd99ed889f0b30ff3e2581a0c9fe77c5f99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4ec6f85a52321953ee44e0f1899755c4501383dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cebbb25028a4830a57371299c3aea9d21c66ad57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:27:01 2016 -0800

    MFGhostIter: support for team and thread

Src/C_BaseLib/FabArray.cpp

commit ab8dfb2c004bf0dae223d89eb73d343237702b9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:06:49 2016 -0800

    minor

Src/C_BaseLib/ParallelDescriptor.H

commit 4304604b6ead17dbad9247d19fa9bd6864d36b82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 17:05:10 2016 -0800

    team_for: rework on support for OMP

Src/C_BaseLib/ParallelDescriptor.H

commit 3fcc8aab027a3b181830ed5567d29672dfc38388
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 16:44:38 2016 -0800

    MFIter: support both team and thread

Src/C_BaseLib/FabArray.cpp

commit 4c13628d19ece8501ab4de3b1245afc8a8463b5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 27fa0f4547b45526f20645dbaf535c78ab19781a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 15:21:34 2016 -0800

    Don't call free if not allocated

Src/C_BaseLib/Geometry.H

commit d36e2ec260c4efad1818abc130f553d59ce9304e
Merge: 740f977 32a4620
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 32a46208f7b784b51f4dcfb24d86efb99a63842a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 14:39:19 2016 -0800

    fix BL_AMRPROF

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit 740f9776f83bf039c4e596164a4d0f15bbcbfc53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b7e4e6520a60eb842a1d6c7c4a99ba4d877d13d3
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 29 13:27:39 2016 -0800

    setVect function for broadcasts.

Src/C_AMRLib/BCRec.H

commit 51005fc56ca1f559cb5116be302c9ec4c560ef76
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 29 13:15:07 2016 -0800

    broadcast bcrec.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit f9e8edde96b1e93d9a18e3729909a73ec5afa6f0
Merge: 83967fb 4f499c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:52:13 2016 -0800

    Merge branch 'development' into pgas

commit 4f499c8797cb5219222f50818ae0e2eac185478b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:51:03 2016 -0800

    removed an unsafe omp parallel I recently added

Src/C_AMRLib/TagBox.cpp

commit 83967fb244b97a04568590119b652036d0f14894
Merge: 4279101 c12345d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 29 10:24:47 2016 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
    	Src/C_BaseLib/ParallelDescriptor.H

commit c12345dd7e48751f981cf064efb6298c8fc43937
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6151c2e04a200ae54f9640220ada51a0a4e5dac3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 42791018b1e0b37efb86750023817c36be24798e
Merge: 1aaf538 bc665e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc665e99e3aca3a248413aa66bbb6f01e83df548
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1aaf5388553558e9dc501b86e3fb812e1e6629d3
Merge: 34c8379 6509c76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 16:50:39 2016 -0800

    Merge branch 'development' into pgas

commit 6509c76640b9c65f80521ec88d87fe1048f0dba6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 16:50:27 2016 -0800

    remove deprecated functions

Src/C_AMRLib/FluxRegister.cpp

commit 34c837916c9eba771629b0ddc2daf3b5593d904b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 80cc7121c5ca14a3e2aecc943a10259a4e5be6fe
Merge: f5268e5 9679fa2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9679fa2b7e128da138f8d300e63dcea2a1551f2f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8f63142bae57878e14f738c7c0bec51d5707ff0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f5268e5f7c028b180e0299e93707f8edadc84e8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 12:43:35 2016 -0800

    Fix TagBox for team

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit b762a609df275f93ecfbb1066a5588fa2fc74dde
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 26 09:50:02 2016 -0800

    minor

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/FabArray.H

commit 0dca9c894b0afc40e0c2dfcc4873c2f854427ad2
Merge: 9ac2734 171766a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 25 16:27:18 2016 -0800

    Merge branch 'development' into pgas

commit 171766adcefde5f577e8ee94851cd256bdda386e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 485b70f91f3b2f470c9ba0b907ac991ea2da3cd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df2d7a540223dd970c774c29ac8e6914cada808a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8936ff44472588d12b325f950ced07804dd1505c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 18:25:41 2016 -0800

    remove some deprecated functions

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 9ac273406e76ad65d5f116cc3629683936312ba4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 18:17:29 2016 -0800

    Owner only in the parallel linComb

Src/C_BoundaryLib/FabSet.cpp

commit 54eaff74aa659a628c7856828f6eb5019dd09bc9
Author: vince <vebeckner@lbl.gov>
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 ff9697f827ea1ab8ddad9000d891e0bbd3790542
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 17:47:40 2016 -0800

    update FabSetIter constructor interface

Src/C_BoundaryLib/FabSet.H

commit b290c0e1912d22f69da25c914f068176637946c5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:07:51 2016 -0800

    added grid redistribution.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 58d81ef7da7d22fc1184a07d818e2e9ff39fa74d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:06:20 2016 -0800

    more broadcast variables.

Src/C_BaseLib/MultiFab.cpp

commit 2c66269a68e28a57f0926bd5124d7be24c853e29
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 17:05:52 2016 -0800

    more broadcast variables.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4ca44e43ea12e4e5eb6e384ce2495e202aff2d6b
Merge: 552a007 654abe8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:24:13 2016 -0800

    Merge branch 'development' into pgas

commit 654abe8edb2b08f875e02c03507730b360114535
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 552a00724a27e19bbc8a6118337933f20ccb9c65
Merge: fe348a1 4644c78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:15:05 2016 -0800

    Merge branch 'development' into pgas

commit 4644c785276e6cbe1e1aa17302ec68a20610ff5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fe348a1494c8ba031854f8f9b4730556b909b91a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 15:10:12 2016 -0800

    comment

Src/C_BaseLib/FabArray.H

commit 0b21218bd627e3c8f84863df3fe8e77038dba381
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e7b87701910294c6f408a3dc4e32ac60a970defa
Author: Brian Friesen <bfriesen@lbl.gov>
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 e500f43cd23f65e6f5fc6df98a2f61d951947ab2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Feb 16 15:09:33 2016 -0800

    MultiFab: update comment on using SendMultiFabToSidecars()

Src/C_BaseLib/MultiFab.cpp

commit d9a99a01f3e1ba8382184dd3cae6f49a94656068
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3cf87eb1d50a2f6bf21f38fe78e67799baef6f7d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 14:00:37 2016 -0800

    added more vars to broadcast.

Src/C_AMRLib/Amr.cpp

commit ac1dbfb39b7df442af65648c289a4695ad6cb5e1
Author: Brian Friesen <bfriesen@lbl.gov>
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 582aac1081ad238e5428724b01698319877e7a03
Author: Brian Friesen <bfriesen@lbl.gov>
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 76a51aabd884560f7407fe69b4f30c72aa76c4a5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3605d734715ab911086415eefc73c4eeb1bcbdde
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 12:22:06 2016 -0800

    BaseFab::swap: swap those new meta data too

Src/C_BaseLib/BaseFab.H

commit f9953e3f12b1584ee5094b0bce3495557305524f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 12:20:06 2016 -0800

    TagBox: should use local index instead of global index

Src/C_AMRLib/TagBox.cpp

commit 7e02e7d6fa07f56ee63ef3ca0d602751eb8d4b66
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 11:29:30 2016 -0800

    moved data declarations out of function area.

Src/C_AMRLib/Amr.H

commit cb9df3f110c347cfc72f83421c793f8753ea712d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0b0c6677deae9a1cac6c89afbf8e32ccb9af312b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 24 10:35:37 2016 -0800

    handle zero size intvects.

Src/C_AMRLib/Amr.cpp

commit 069c5338bd2fae288f58af6e5a54be7e51f3829c
Merge: 4f22284 323f1d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 24 09:52:20 2016 -0800

    Merge branch 'new_fillpatch' into pgas

commit 323f1d52bccc1f58bbb49d164965256c4ecd815d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8d51a3d51dbe629f25926d1082880e87b1563c2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9c6922ddeec9a8c488e87e5bb953859ef47ba38f
Author: vince <vebeckner@lbl.gov>
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 0695fb9076e5e79abda3992e540f6e9ad5594f44
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:15:10 2016 -0800

    whichProc option for CacheStats.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit ac5e56d4269b23205e5356f1ccd581d7da3ff90f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:09:01 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_AMRLib/ErrorList.H
Src/C_BaseLib/FabArray.H

commit 5d418d70127e0d35c04d1efb89fa7e4bd1614736
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:07:07 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_BaseLib/Utility.cpp

commit 1e60eacb069159be9f25e70d839c48819c3320e3
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:05:30 2016 -0800

    option to add map to cache when defining with Array<int>.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 5d37f8088fdcc9ed63c48660ac44339546502628
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 22 15:04:43 2016 -0800

    code cleanup.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/StateData.cpp

commit 4f2228466a193ffc72d72ce9065e331824279785
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 22 12:24:51 2016 -0800

    comments

Src/C_AMRLib/AmrLevel.cpp
Src/C_BaseLib/FabArray.H

commit 2cf03e656a3ee6dc9b32ee9a6248d1f5435242b0
Merge: 9aff113 227c307
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 22 12:20:33 2016 -0800

    Merge branch 'development' into pgas

commit 227c307e7e4df57343b9b008af58f639a52ba90d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 18:02:14 2016 -0800

    use quiet nan as safe bogus value

Src/C_BoundaryLib/BndryRegister.cpp

commit f23802497c7f500c7b675535bdc50497e8b8f4f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 281de0835e9d0db3b1162981231ce65ebe148ef2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 17:23:17 2016 -0800

    tidy

Src/C_AMRLib/AmrLevel.cpp

commit 9aff1133c605bf66611b5f59aed6563fb9a1e0c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 16:04:07 2016 -0800

    DistributionMapping: Support for team in KnapSack

Src/C_BaseLib/DistributionMapping.cpp

commit 27208bf299f76a83501f39e10d3e1b5bc10a0043
Author: vince <vebeckner@lbl.gov>
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 c3dab281ac8d94b8b7e9d57c146d4983ac03e88b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 19 15:07:59 2016 -0800

    DistributionMapping: Support for team in RoundRobin

Src/C_BaseLib/DistributionMapping.cpp

commit 880cafc49b8a6c382adcb6062187e69c7c84ac57
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 19 13:56:02 2016 -0800

    print allocatedFAPtrs, remove unused maps.

Src/C_BaseLib/FabArray.H

commit 4ffde430c2ac3ce874a222e901caa51ac719fc86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ed7904779e0d3b151dab548cf6b8c4e3849aada9
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Feb 18 18:15:45 2016 -0800

    Uptick tag

Tools/CMake/BoxLib_Version.cmake

commit a78901fa1ecf5e8bfa2324871f8ac2f0c0bc7d17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 16 16:42:38 2016 -0800

    add Team support in CPC

Src/C_BaseLib/FabArray.cpp

commit e38c2419eb4a6f1b8b26af148ed738c3f237ea20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c88514af6d23ad51add2ebecbe9916a0a5b94f82
Author: Marc Day <MSDay@lbl.gov>
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 edf51e04af7138210ff97a0ea67cc79e4e5ef652
Merge: 1863c3e 325681b
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 17 08:40:30 2016 +1100

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 1863c3eb5c833d45c3e3dc0fd79836d3cbab57a0
Author: Marcus Day <msday@FyrHead.ad.unsw.edu.au>
Date:   Wed Feb 17 08:39:20 2016 +1100

    PGI doesnt know about fegetexcept

Src/F_BaseLib/backtrace_c.cpp

commit 04811ca59af78eb7ad11a3e60faf101f3cc1fd1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 89a8fbf9fafdd8b3dc739445287cc4ac2c98e552
Merge: e66b967 325681b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 325681b687d75446274c1e5d2f1b46a17bdfd47f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6ce4758ce2ac9c0d822734e52491807652b9b902
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 eaca6d91abd090f99faf1956223199be5395f3cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a5554903a4a566d96a1f7477b216a71514bdb90d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e0f0c82b3fe7074358c904d568cc7a06a6eade78
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 d3763b7354ad07a4db675a1b4b40e51c4700defb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Feb 14 20:59:46 2016 -0500

    some png tweaks

Tools/RegressionTesting/testnew.py

commit a878bf842517b9370260335c6c0e52324f2629d3
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 8edf1357e3c10e9e7654d803d82cd2823ce979cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 18:55:06 2016 -0500

    fix a few uninitialized vars

Tools/RegressionTesting/testnew.py

commit 1cfc9152db462394609790da027d40a0f97e6477
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7d1d4dc934c2bfc582663b57797cf1e2c0505f85
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c8e8bb73fa9a7e98cfc829a709151bca7c364388
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:21:52 2016 -0500

    more error reporting

Tools/RegressionTesting/testnew.py

commit 8116f7fb9e5c8359ade543a1c72be6aded6b8357
Merge: 03a0a2d 0e2731e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:16:36 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 03a0a2d3f640c688eb8b1ae8da2a7211c070b764
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 15:16:29 2016 -0500

    some failure reporting

Tools/RegressionTesting/testnew.py

commit 0e2731e0f480271dfd821962ef16ef648ea8ca69
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 14:52:19 2016 -0500

    clean up some error messages

Tools/RegressionTesting/testnew.py

commit 2db9aff4d88116641b8514fc432ab976667ccc7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 02787bb80fed324e8dc05fcdb4a7a3cb41ea7417
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Feb 13 09:54:36 2016 -0500

    remove some print debugs

Tools/F_scripts/write_probin.py

commit 2f554c3338be422ea556ca6184803ef90a273283
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3d32a22ca896e665673710a964fe74aebb61c931
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d0171c969d240326e469c917c414a9e952abf901
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 18:35:31 2016 -0500

    this isn't used anywhere

Tools/C_mk/Make.bgl

commit 4c0daae6431889b145ab94edb46511d8d720e57b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 18:17:43 2016 -0500

    remove carver

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit ec3453fa499719229ebe6d37a95c1a8e1505c6e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b7416c7e2dc3a381cb1918ddf68fe4e2eda42ae0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2214b1738749c416f7a0490ddfe76a54d62b34af
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 0177f40fe01f1ce872f160566b46c7c6bbed4e9b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Feb 12 14:07:02 2016 -0500

    Carver is no more

Tools/F_mk/GMakeMPI.mak

commit 8a841a0eec5ea4c3e0330beb771a4c9fce9e0bb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 4e81065d14eb29a9d298923d73eb7388a73c73e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 22930fff0ee70ed4406053d60f9cd7cabf3c49c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 22:52:49 2016 -0800

    minor tweak of get_fpe_trap()

Src/F_BaseLib/backtrace_c.cpp

commit 4176dcdca8f6e70549b29f5304aff34ae203506e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 11 22:43:01 2016 -0800

    remove debug print statements

Src/LinearSolvers/F_MG/ml_cc.f90

commit 86f643ad42eccb81c6da7bb3e93bee1ecf73ee83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 712bf7b73d38856550ffeb8efe0be60d66e1a969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 70dd43e8c6ff7784909fc5d5c7f77ee688f8ba69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 90b2c8e5e3587bbb42a08706d26bedee38d7511a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 00e950599ceacc7e513323c1ec7708965d423d45
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aa6395002c01941e8b8453cfede3e7ac23d6a449
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 cac82c1b05c2b12665640d8e5fb86f786513873f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 aa55f15776fa0563f63cf6ef79416b76662986ff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 13b77f5f6fd60bd377899978e81f352ff7810e01
Author: Marc Day <MSDay@lbl.gov>
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 84aec60abb4ea46f4b51d04e1faab114236c3cb2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 10 13:54:12 2016 -0800

    Remove my debugging line in the GNUmakefile

Tutorials/MultiGrid_C/GNUmakefile

commit bdb062473ad807f250da6fce70229613e19b8051
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 10 12:27:25 2016 -0800

    finally fixed my new bug in INTERPER_3D

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 63ef1c86cbaa2af51e964a521f8bb403da840bf8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 10 15:23:18 2016 -0500

    fix boxlib-only runs

Tools/RegressionTesting/testnew.py

commit 5c8f75874059644e782b65f60c48db97ac524c53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6188817c2fe6f95634875344630b4a86655b4b09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1adca55a4e04c97d01b6728b7bec376a96289155
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 9 15:25:54 2016 -0800

    avoid nans

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 196323f684226a391110075abb47e58f72584d1f
Merge: 7a0b1b8 b529f4a
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:56:38 2016 -0800

    Merge branch 'development' into 4thOrderMG

commit 7a0b1b8a3a4c9830ee101dfa5aa4f7f8d5e21047
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:56:08 2016 -0800

    Change default

Tutorials/MultiGrid_C/GNUmakefile

commit 2601815504334801f3d8d7a3511d3dcecbf7822a
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 9 13:51:37 2016 -0800

    Final junk

Tutorials/MultiGrid_C/main.cpp

commit b529f4ae7def727e56a14f4c8edb39342bb22e25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 9 12:50:05 2016 -0800

    avoid copying nans

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 02f69fdd1dd45a1b8ed082b893534805f650faf0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 9 11:56:30 2016 -0500

    fix the backtrace links

Tools/RegressionTesting/testnew.py

commit c6f451a52ae9064e8d7a1af6ae4f4247337faf02
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 9 10:48:43 2016 -0500

    fix name clashing on the backtrace files

Tools/RegressionTesting/testnew.py

commit b1de40b0e6a253c4330def0c46d3da1987e82a06
Author: Marc Day <MSDay@lbl.gov>
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 e83053ab53df7fb42ef2458e3cd3968bbd2afc9c
Merge: 6b010a4 5f93403
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 21:08:33 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 6b010a4c37bd7d354790716b34e1e8cc94249f09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 21:08:21 2016 -0500

    add support for copying and posting the Backtrace files

Tools/RegressionTesting/testnew.py

commit 5f934031a10d1639032e95f61d9f591cc9a123ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 8 20:17:53 2016 -0500

    enable TEST=TRUE in the tests

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 4dfbb89382de6a4c77936db83358675322d18656
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 49f3551e2cdf90fd99bcff9c37449e5436a4671c
Author: Marc Day <MSDay@lbl.gov>
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 3588512b7eebf0c4edcc8d91e4747f5a7d54cec1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 08dfb7a7748f8aad777cd092f3282829b73e0dad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 15e974d91ffbc44cf79bb612f08bd6720cbfd836
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9c6515e8ed6a89d96039f320f38324bdb3701285
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 710ae0342614140bfe0c63da47e21689b9c9a7c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5d6637d94e55a20292f25c4beac0c2418278c623
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fd61d6ee07ed5a534046c421904640de9ae8b62c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b8b9d6e1e344aa8887998c947c60c3378a8d90b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 12:17:02 2016 -0800

    update Readme.backtrace

Docs/Readme.backtrace

commit 920bcd76b9275dd9e8422d6029b09b66de5c25de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 974b799cbda66eaf782ad75ab003cd6c7781fd85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Feb 7 00:41:57 2016 -0800

    Fortran BoxLib: define BL_TESTING in DEBUG mode

Tools/F_mk/GMakedefs.mak

commit c75463e66358cd748b644d77be4c462b91a995b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 65fd7d9747aeaf29f36bb96d612090d4776278fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b5ba06701659e89c28a2811fc1d1d30745eadcfe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a912ac1ea2d07d7991a3076abb5247dcf1ec3939
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6371b62da50777e8bba8238e3b333831cb1a6f9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Feb 6 22:56:00 2016 -0800

    Define BL_TESTING when BACKTRACE=TRUE

Tools/C_mk/Make.defs

commit 3120098dc7260b4c54339f7cad0a119bcef40e0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 754cb4f6e9ef548cef7f52227b96a0b028b46132
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 004288f34e69a5059a3ca342b58233d749d4ddb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2113b4c6cb1c8137bd61bb2de6d02a4b5b628708
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cfe01390c3442ca6c86de58c5e4a575ae8053f83
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 da2638a0c79e79bd754a43c33da9010804c92e34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d928d0d6f67f4ba55a70e53b3f5e7cb98b101cbc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9cb739cb4a81abeb988db6d228c51ed7cea274c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 69af8db19b507c18273b9a62d2b7deb868cf104e
Merge: d9e0ece 0de1681
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 4 17:51:42 2016 -0800

    Merge branch 'master' into development

commit 0de1681280d937af895733ee52847c1154edefca
Author: vince <vebeckner@lbl.gov>
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 d9e0ece560c51ae038319a80b06b7d3b25dcf037
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e66b96731e9f7c633bb78e80d9fce6f6f8278c8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f0551107b49ece3f0dd373ad5996356b0c76d235
Merge: aeb94a6 c8aeb90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 17:22:31 2016 -0800

    Merge branch 'development' into pgas

commit aeb94a6a825ef9a520782be044dae0f07bd64a9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 17:22:04 2016 -0800

    clean up FillPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit ed1278d533e357fb8377c6d651d6584d0cc876d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 834e3f962d4b6a6c1a02bc0dd6c51a987942ef81
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c8684005ecb43fa207eee976ed662a46dcd4d9d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 14:11:37 2016 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 6640fcbcb6b46d02ebde53cfb17e51f4481717e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 13:26:27 2016 -0800

    test-mpi3: write and read

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit 9bc80ea2a4804e349293bd73e5e9a5c9d4d555af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 13:25:43 2016 -0800

    fix a typo

Src/C_BaseLib/BaseFab.H

commit 2256051dd9a7490a553bab9594317198293a9ba7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:20:23 2016 -0800

    fix typo

Src/C_BaseLib/FabArray.H

commit c3f590ae62c2a25dfba92858d33f8c36e6f0d632
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:19:04 2016 -0800

    minor change for consistence

Src/C_BaseLib/Geometry.H

commit 432ee30e8a1cdc383c1cef5212a594b42bc49fe9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 12:18:50 2016 -0800

    another BL_USE_UPCXX --> BL_USE_TEAM

Src/C_BaseLib/FabArray.cpp

commit 336115c997dd0003db8e578892f39cc509754c0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 470ef6a20fa61121ae3ad9c560ea23eaa9c280e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 2 11:22:22 2016 -0800

    add more Memory Barriers

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit f9ff1cab3c624418e2d6658991618f0d5a0c9f0b
Merge: bd65fd6 c8aeb90
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Feb 2 10:45:59 2016 -0800

    Merge in process, mg tutorial does not yet build

commit bd65fd65a2d455b15cc5a81e6dbbd8af670f8d85
Author: Marc Day <MSDay@lbl.gov>
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 dc31be63864bd2299fa5e83848b0c3fcce3e2f71
Author: Yili Zheng <yzheng@lbl.gov>
Date:   Mon Feb 1 20:44:14 2016 -0800

    Minor fix of test-mpi3

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit 0be7b7d7162eb00245b233ccea44c6348596e996
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f0460b90d97e061e317e9c5d9436d595e5d5b2b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 19:57:23 2016 -0800

    need to pass T** to MPI_Qin_allocate_shared

Src/C_BaseLib/BaseFab.H

commit 474d67af817b22b8638998c34f67cf9ae65be18a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 19:56:33 2016 -0800

    update ifdef

Src/C_BaseLib/Geometry.H

commit 82cdf87adc7cc3bc2b4ae65f415a0e442370b42b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 17:34:45 2016 -0800

    testing mpi3 shared memory

Tutorials/PGAS_HEAT/test-mpi3/main.cpp

commit c5bafe141b88e561ea7a1cf053c71e772a3119e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 16:09:52 2016 -0800

    fix ifdef

Src/C_BaseLib/DistributionMapping.cpp

commit 39c1d4e4bb88e19f182773d450ffc23993dbc26c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fcd1f4c2c2884d2f6533378591b04cbe560e0c79
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:38:42 2016 -0800

    sync sequence number.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit a6000dfedaf7d941f1090f65c5720db64c8ce73d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:04:45 2016 -0800

    braces.

Src/C_BaseLib/VisMF.cpp

commit e00190c13e7bd51acbaf958150db9963fd571da7
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 1 15:02:37 2016 -0800

    reset noutfiles.

Src/C_AMRLib/Amr.cpp

commit 0092622761e866bed1aa8c71c00c868a29bc06ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3f58371f946f860f82086191f12d14e58720983b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 62016c9a10d1e14fdd2bb2b40944a6688f97aad8
Merge: dc3358a 9c6f042
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 12:41:09 2016 -0800

    Merge branch 'mpi-onesided' into pgas

commit 9c6f042010c19e40625e364129e74901b710a190
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c8aeb9055c6cabf09bfbae4872b2decc14631e3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 1 09:02:03 2016 -0800

    fix assertion when DEBUG=FALSE

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 23f5b06313b2466bfc81cb77aaa9e99d435eae54
Merge: 57289e3 24d7dd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 31 20:36:28 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 94f82bc2d0ed96f3a170b4e35162cc9481b2619a
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 19:05:03 2016 -0800

    sync sequence numbers.

Src/C_AMRLib/Amr.cpp

commit 7afc06c45fc22a5dcde88886c5968e417e1c692b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 19:04:52 2016 -0800

    sync sequence numbers.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 9b13e4face283edf2740a22d61e18dd4dca44509
Author: vince <vebeckner@lbl.gov>
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 24d7dd15fa2a5866e2af0cd8be0f8efb24e315d0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Jan 29 12:16:53 2016 -0800

    Remove unused variables.

Src/C_BaseLib/Particles.H

commit 27ff264a3eb527d0822ec26e707a2c9127a9433f
Author: vince <vebeckner@lbl.gov>
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 9510a09703add2dce17c062831ca5a7373b20212
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:35:08 2016 -0800

    also bcast coordsys.

Src/C_BaseLib/Geometry.cpp

commit c43a79b3d5e7b593a70ef112fcca0c21533d6f77
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:33:34 2016 -0800

    some name changes.

Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/MultiFab.cpp

commit 12318172c133b4e049117fc2b290909d7fa2fa4d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 29 11:30:54 2016 -0800

    sync distributionmap caches.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 8a5a9444e640f07302dc8620b368c636d05a8ce0
Author: vince <vebeckner@lbl.gov>
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 dc3358a82943bd0698d53cee29b65877d85fbc5d
Merge: b17f3d8 4c8f3f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:49:46 2016 -0800

    Merge branch 'development' into pgas

commit 0b1e42611ca90e2e1d686514cefd6588047167fa
Merge: 0dfc5ab 4c8f3f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:49:15 2016 -0800

    Merge branch 'development' into mpi-onesided

commit 4c8f3f780d5f926bed876c0b306898f874e31f15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 14:02:31 2016 -0800

    Particles: fix array index

Src/C_BaseLib/Particles.H

commit cd5951d3a64f9d42e8447f9c1847b8f7539191d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9ce2cab94c59e1b9abaf7386e54883763097d86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 13:44:18 2016 -0800

    Particles: add ParticleBoxArray() and ParticleDistributionMap() to container class

Src/C_BaseLib/Particles.H

commit 51cdf303869219150e8af9fc1170ca802b1e8774
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:54:34 2016 -0800

    func name changes.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 6fae764918f4a7f9ae6114995cb0c5470da831c9
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:54:13 2016 -0800

    func name changes.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit a7a1a8fdd62a86f97c6e957d81df13890dd94c95
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:50:39 2016 -0800

    func name changes.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit f3acf2018d95912f1c88cb264cf79eb4265d3577
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:16:51 2016 -0800

    some cleanup.

Src/C_AMRLib/TagBox.cpp

commit 5afadbd2b912f92395d9e8e4dae4a8568793309e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 28 11:15:51 2016 -0800

    some cleanup.

Src/C_AMRLib/StateData.cpp

commit a85fb028c48d5937238cce60b5edf3cdd7244273
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 28 11:11:57 2016 -0800

    MemPool: minor clean up

Src/C_BaseLib/MemPool.cpp

commit 64adc50a0a6b6c7065a8e68a8644602b66c025da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f786b5bb5d814a90625ba6eef5bf4969a2422c99
Merge: 44dcf02 dde9a71
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 27 16:48:47 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 44dcf0261a754cb94ff3838bd64f016c0cb14864
Author: Ann Almgren <asalmgren@lbl.gov>
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 5288cb4598d167421ec35398a2768db335f9e29b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 27 16:02:58 2016 -0800

    tests for broadcasting and (un)serializing classes.

Tests/C_BaseLib/BcastClasses/BcastClasses.cpp

commit e09f798238a57516a28fc2940f69a6c7753014c5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 27 16:02:01 2016 -0800

    (un)serializeboxarray.

Src/C_BaseLib/BoxArray.cpp
Tests/C_BaseLib/BcastClasses/GNUmakefile

commit b17f3d83e521eaa32f085af3c4a8da0372d123ec
Merge: 0dfc5ab dde9a71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 13:19:22 2016 -0800

    Merge branch 'development' into pgas

commit 0dfc5ab89b98014d83e506bd90294a3ce12e9253
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dde9a7117c4760baf04cec1240bb1ccd647d0fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0201aeb11d37c41a8cbc5827b1abc93252352dd6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 710988befacefae14ae57ed0d49de093fafd42c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 27 06:20:03 2016 -0800

    fix omp problem due to recent renaming

Src/C_BaseLib/Particles.H

commit 893049c2882147fe645d2bb8e33006d12928796f
Merge: 2e1617c 74e389a
Author: hongzhang shan <hshan@lbl.gov>
Date:   Wed Jan 27 00:17:55 2016 -0800

    one more timer

commit 2e1617c07ed783cc0437a0ed938c4be9bf64d376
Author: hongzhang shan <hshan@lbl.gov>
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 9512e0cdf3bbb7038e0a2ea057f83d38d973c341
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c814cf42f16f862ee495bc495a8d36be4e1fb7f9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a23b2e0a8dfbe3d5e549494cce50d09c67cce452
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bfa7647c31aa598f963246b97252b1c92f3a10e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 74e389a497f7562e17a6d3f431db8c96134a970c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 16:24:39 2016 -0800

    remove a barrier

Src/C_BaseLib/FabArray.H

commit 5d7d2b69f5847b7e27d82626244b3e8fff90f7b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 26 16:23:41 2016 -0800

    fix typo

Src/C_BaseLib/FabArray.H

commit f06cefb1721745660c956501af8cad75f4342755
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eae5cf3abfd165e4a3eda156e62b7b6048efadc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0e1706c79f61ec6b984f0bcc726230c1837fb5b8
Author: Ann Almgren <asalmgren@lbl.gov>
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 df2acc76e803fadbd86ae590bbe439e07d727a52
Merge: 345e302 bf15ebc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 26 14:15:16 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 345e30211e027b1f85e5ac7e7173bce450ebaff8
Author: Ann Almgren <asalmgren@lbl.gov>
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 bf15ebcd753beaa055ebc28c52c4adc6347f672e
Author: Marc Day <MSDay@lbl.gov>
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 3a1001538f7918751b7f9f4d51152bc87640a26a
Author: Ann Almgren <asalmgren@lbl.gov>
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 265b866e05035850f9dde1ed2a5f7e5fe9bebd19
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 25 15:21:59 2016 -0800

    broadcast functions.

Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/CoordSys.cpp

commit 54e97df5aea24bcce5b25e9f52291217fc4c9a4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8038072657d880a45c9098ded332c5fff4538171
Author: hongzhang shan <hshan@lbl.gov>
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 f59daa05d0f7adfab8e661a5ef225812ecc68464
Author: hongzhang shan <hshan@lbl.gov>
Date:   Sun Jan 24 15:52:08 2016 -0800

    fix isend error

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 57289e35d4fc3ce5847a16268557f5b6366a47ec
Merge: 3d3ce91 523548d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 22 19:39:13 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit f33fadb9dd0acfd2f91cd101386e13f78241dbc0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 22 15:16:41 2016 -0800

    USleep function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 2991fbd920af9fdac1e2b256292660c12c068a02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 15f9937774b5295859ee0de6d06675de2057752c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 523548db65a0172e7cc3508cd8b7af73487c898b
Author: Ann Almgren <asalmgren@lbl.gov>
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 54b356f8dc662e5450600995425ffec5b0518df2
Author: Ann Almgren <asalmgren@lbl.gov>
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 79993232268e168424f5d0d10417965cb4c96060
Merge: f9d2c72 8c61951
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 21 14:28:19 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 0f90451119af33ced46416acc462f3bc4396a293
Author: hongzhang shan <hshan@lbl.gov>
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 8c61951f091afc37388f363506480f760e0ea6c3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:32:44 2016 -0800

    the makefile.

Tutorials/DataServicesTest0/GNUmakefile

commit d424f67e486cdfac39459ed5d19a6d4b022e3aa6
Author: Hongzhang Shan <hshan@lbl.gov>
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 f9836086648329ac542257cdffa754aaae0e400b
Merge: 13b3284 cf6ea96
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:14:41 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 13b328413731f48fcba7176699649425560e207b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 20 17:02:35 2016 -0800

    A simple tutorial for DataServices and AmrData.

Tutorials/DataServicesTest0/DataServicesTest0.cpp

commit cf6ea9667a427565b9d402b6cb9cb6a860774896
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f9d2c72a60a50baafba9e006b4b831b49fa052e1
Merge: 7ab8797 34598ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 20 10:59:42 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 34598efcb6f44eb9ae9065a7310e121938f1e7c4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jan 20 11:19:42 2016 -0500

    add plot of rad sphere

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 952d8282e013fe269851904c36587df7cd6e177b
Author: hongzhang shan <hshan@lbl.gov>
Date:   Wed Jan 20 03:24:52 2016 -0800

    version 1

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 39eff4106c00d387db0aabe667919366f4dec7b7
Author: hongzhang shan <hshan@lbl.gov>
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 733fa407e36144222192a9ed18d324f461c59fb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aa46da3331c03cc2722840bfc8de3606a082384b
Author: Hongzhang Shan <hshan@lbl.gov>
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 7ab87975c58f6547b207b5babc8afd7d53b32dd5
Merge: 77aa394 3b7ef3e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 19 12:06:31 2016 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 3b7ef3ed285136779dd385d7221ec7ed796d3e14
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7f628f149d114a39f791491291d394aeefea66cd
Author: Hongzhang Shan <hshan@lbl.gov>
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 3d3ce916105b3f48d08cdf44b552c03e6298014c
Merge: 0df95b5 c2fb987
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 18 13:27:17 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c2fb987f8785fe7b1e30c617a9ebb8c851d1c80e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 16:47:51 2016 -0500

    use font-awesome

Tools/RegressionTesting/testnew.py

commit b6abbf56fd1d23d55cf9e066bea8b81c4e56ae84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 14:45:54 2016 -0500

    add timing plots

Tools/RegressionTesting/testnew.py

commit ddc6c587eecf23476ec3180cda538d577b17d79d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 0df95b53dadba8645d807b1743f36603544ceaa4
Merge: ff6af7e 30aceea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 17 12:04:58 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 30aceeaa9e98725b9ce47fd5199689fabcc5059f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 16 15:16:09 2016 -0800

    more interfaces to bl_allocate

Src/C_BaseLib/mempool_f.f90

commit ff6af7e09cb4f98785638b3b99f745412a63e012
Merge: df53743 a79903b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 15 09:37:48 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit fe075152b75230aa84a44806e17c10e7e748f287
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e667b3b4cf0b35fc34def231248faa136468cb2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 af09e176368ee5fe917c3bc0d7b16693cc2c1302
Merge: da6c330 a79903b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 13 08:47:12 2016 -0800

    merge

commit a79903bfee85feff10e68c6b7b8c39906615135d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1afd18526f7616f95fc685a5e8e1640d46d173fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 16:50:11 2016 -0800

    add FabArrayBase::empty()

Src/C_BaseLib/FabArray.H

commit 12d04b363b76dadff7b5dbb8ec35922fe87e467e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 12:29:10 2016 -0800

    add AdvectWithUcc that advects particles with cell-centered velocity

Src/C_BaseLib/Particles.H

commit 858fedf3c42fb2c668a4ceb8c806d74b70eb119a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 12 11:30:14 2016 -0800

    AdvectWithUmac: fix boundary

Src/C_BaseLib/Particles.H

commit 827d0c747821c921a2bb4e816500a858ade9bb1f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 11 18:12:48 2016 -0800

    remove an assertion

Src/C_BaseLib/Particles.H

commit 729dcd13ed18491407478ab25474cd37a0be3b0b
Merge: b529ad9 3dc0793
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 10 15:31:24 2016 -0500

    Merge branch 'development' into preprocessing

commit 3dc0793ecb1b2ad33356cfbe85e6e1a2837ff844
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7e4785917a4cf07e0e40a912efc6d5f43da9cc9e.

Src/C_BaseLib/FabArray.H

commit af42e2ec1240f7676763bec0d287142927614d55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 8 10:07:14 2016 -0800

    fix bug in my recent change to SumPeriodicBoundary

Src/C_BaseLib/Geometry.cpp

commit 0c37513b6084010f56ad8a8d101e17b7338ce360
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 8 10:05:36 2016 -0800

    fix bug in my recent change to SumPeriodicBoundary

Src/C_BaseLib/Geometry.cpp

commit b1659eb5429665c7e935b11914ec04737a5be116
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 21:10:46 2016 -0800

    add comments and tweak Geometry::FPB::Operator<

Src/C_BaseLib/Geometry.H

commit 3ffecba0d07364a294071e396cb9b99df0930b96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 20:54:09 2016 -0800

    comments

Src/C_BaseLib/FabArray.H

commit 7e4785917a4cf07e0e40a912efc6d5f43da9cc9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 17:29:11 2016 -0800

    no longer needed

Src/C_BaseLib/FabArray.H

commit 419c1dcd99d67dff72e37203f3144869f65e5509
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 17:28:11 2016 -0800

    Optimization of SumPeriodicBoundary by reusing the FillPeriodicBoundary cache

Src/C_BaseLib/Geometry.cpp

commit 532d1102d579872e14b13adba08bce49c86e8e03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 15:57:47 2016 -0800

    readablity

Src/C_BaseLib/MultiFab.cpp

commit da6c330834da9e17a080743d66c5761c08cc8ce5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 12:34:37 2016 -0800

    minor clean up

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 2abd16a3ffb09e767993a780d58e7cc6c47642b5
Merge: 8865c06 e0fcd3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 7 11:16:19 2016 -0800

    Merge branch 'development' into pgas

commit 8865c069e6f9918dd572b88cae809ed21a1749da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4d40b0a37a0ca6d7835f44de0ab4b0212f69c764
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d107a037a0b2ebbc054bda6014968324307b9624
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e0fcd3e45d6d9c1c9ab97a8f201427a9300cf4ce
Author: Changho Kim <changhokim@lbl.gov>
Date:   Wed Jan 6 14:44:49 2016 -0800

    f90 codes do now work on cori.

Tools/F_mk/GMakeMPI.mak

commit fd0c441fbbe0448466375f6ecb6a3c8f5647f815
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8608bb6fdb5960b810967281bad94b7dd95932ae
Merge: 622c874 31b5414
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31b5414d3d0a0411238c62d73e93a53ce6475bbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d7b19f0e9c922c6683daeaff689964ab1147ce81
Merge: f8eba75 9f5b879
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 5 18:59:38 2016 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit f8eba750d827bebc787507831a067d76de9ca619
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 5 18:58:58 2016 -0800

    plug memory leak in multifab_sum_boundary_c

Src/F_BaseLib/multifab_f.f90

commit 9f5b879a42cb6240f888eeb32b311b6647ffe631
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 88f5540c59e861997c1445ef2f92f6ccaf0bc7b9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jan 5 19:25:53 2016 -0500

    update usage

Tools/Postprocessing/F_Src/fextrema.f90

commit 9bae1d1a79c78c43c79374ed285b02376eb0f0e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 5 15:37:09 2016 -0800

    clean up

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 622c874ba237972db135387e1f841e4fd32f869c
Merge: 2b7e5ab 5c7de19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5c7de19dfed3ba57070052fcce99f5541085ccda
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 759ac5ef540fdfc6eed5c9f7236613bc278885c7
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 5 13:21:11 2016 -0800

    call bndryreg function.

Src/C_AMRLib/FluxRegister.cpp

commit df537433279438ba6ff61a1a41425e1b978cfab4
Merge: b529ad9 d8f0efc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jan 5 10:45:14 2016 -0500

    Merge branch 'development' into preprocessing

commit b529ad933ed95f93e077554e02bf832d1220093f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d8f0efc7be1b9ceb613a6547720834c1cbd6376b
Merge: 29769b9 322d94c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:12:50 2016 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 29769b940e9fe7d00503af80273bd60d9e0a4c93
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:12:40 2016 -0500

    new source format

Tools/RegressionTesting/Maestro-tests.ini

commit 322d94c8c78efa5de46557938e7503e0b049f684
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jan 4 19:11:23 2016 -0500

    add the Detonation test

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 77aa394cfb5ae273769af9b07fc9227be7b51a44
Author: Ann Almgren <asalmgren@lbl.gov>
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 fc0cf7a3a455c62be794faa957992b84144a1bca
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 bf48920ba89657776545555b5f8cac3ecb469f43
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 62df90774772030699457d2c424494b0d52b7c28
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e207f77fd02221483bfae6848787a8c7050a8995
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Jan 3 22:08:03 2016 -0500

    remove homer

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 035b871990d8d0981aff472dd0bef9cb0694660b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4a305a3c07b2bccc3e5163a244d60a919aab93ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5ed5a54454186a96f0093262fe96c60fa2519f6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a9745113adaecbcd36a136800c17f9988679ef43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 13:52:00 2016 -0800

    keep boxarray hash

Src/C_BaseLib/FabArray.cpp

commit 39bf0ba6670d99d08f06bdd60b37a29ce921f2e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jan 2 08:19:15 2016 -0800

    comments on filling periodic boundary

Src/C_BaseLib/Geometry.H

commit 2a53a33a6b1610b277191842bed63032e0a61987
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 20:28:40 2015 -0800

    minor optimization

Src/C_BaseLib/FabArray.cpp

commit 6738eb2b1dc9b293c76d8bffda6a5439cad19f99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 20:28:09 2015 -0800

    make it more readable

Src/F_BaseLib/layout.f90

commit 1c4a907ab1e8f6026f2c552a3536f8f3bfebb99b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6c31a7b36a2ee0b590e002bbf7078625d17015cb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 73075be8c85bf8388c7d49953baea8c1bacaf2ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7b1153d6d5ab14eee38ce5025099847672576455
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 13:46:52 2015 -0800

    tiling in local copy

Src/C_BaseLib/FabArray.cpp

commit 8856b3f051899bc9328a589837b3cf8c5be82b64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 12:40:34 2015 -0800

    optimize box-box intersection for parallel copy

Src/C_BaseLib/FabArray.cpp

commit bc0c75cdee8eb1b1634bc65a97042a98c27ec248
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Dec 26 11:59:59 2015 -0800

    fix thread safety in FillPeriodicboundary

Src/C_BaseLib/Geometry.cpp

commit a9d29ece4c151ca2d8656e128099502b9cc35c3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 738e15570f93a3cf8ee5e4df29bebd3d332af032
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9d53e95bd726632d465a2b477320b6e673b045cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6e5299540757c6f91bd3a436f798f8bf705e8236
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 3f2dd5099d73f5eeb532944491965f52bd964497
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1136ab8b98ee17bfa9c84457ccc4d650b402d5b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 17:09:46 2015 -0800

    tidy

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_nd_restriction.f90

commit f7374e26c6ead1e5cbd704ce5d49fc068380c964
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 21 13:12:52 2015 -0800

    removed some temporary layouts

Src/F_BaseLib/ml_nd_restriction.f90

commit e652cfbb8d2a6305f0e4f178303a0ec6c81f08b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 49406325ad97e5aafd77ccdc632e595c8e20e8e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 119a00f7d10dcaea937d23ed7ed8ed53fac2d633
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Dec 19 14:17:02 2015 -0500

    Fix incorrect query for small_plot_file_root

Src/C_AMRLib/Amr.cpp

commit 58309e931af0a81bac57bf2b3715822a36bdaec8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 18 15:46:15 2015 -0800

    move the setup of signal handler after MPI_Init

Src/C_BaseLib/BoxLib.cpp

commit eced9dc9e36ddd4eca4fa305b6c7b1efef506f09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7c97595a1806ebd492d4d3db7d64d85cb5d8686b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 501f1156bb2782bfee83f53f4741a1fa76cc7e71
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 17 17:19:19 2015 -0800

    make the output more readable

Src/C_BaseLib/BoxLib.cpp

commit 54b884744ab37fad92cfc3063f8d49ae63e3ba88
Author: Ann Almgren <asalmgren@lbl.gov>
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 804aef575506abd9a5720b73a7bd272bcacefee5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b7cccef911eac5323022954dd5d2db35e6c169b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 16 09:13:48 2015 -0800

    tidy backtrace

Src/C_BaseLib/BoxLib.cpp

commit 64eecac545c0d01ccd052c849ab40a0c36bb2607
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:51:06 2015 -0800

    print out more comments about addr2line

Src/C_BaseLib/BoxLib.cpp

commit 618afb0a01270074174725ecbc7a2b78984aa9b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:21:14 2015 -0800

    Particles: fix a memory leak in AdvectWithUmac

Src/C_BaseLib/Particles.H

commit d9019b1cc848373b31afa11973a818a15ac04664
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 15 16:07:51 2015 -0800

    clean up

Src/C_BaseLib/BoxLib.cpp

commit 6150e6519bfd27ee2158c85497141209f11bea2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 848478ea2d3a4719da101a8d21769c427f78987c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8785d94c6dc07619ed7d55d1fbd40d5b4f33e80b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 18:37:29 2015 -0800

    MakeSidecarsSmaller function.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 5b7ea38165deb6214af12d622039511f50c9e7ce
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:08:05 2015 -0800

    promote MultiFab::MakeSidecarsSmaller

Src/C_BoundaryLib/FabSet.H

commit 0043e97c33c3925bbef8ac2d2a84970400ed0c24
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:05:01 2015 -0800

    MakeSidecarsSmaller function.

Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BndryRegister.cpp

commit c9772e3568a7f1a8f3345ae6b8dcbd8062e052ea
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:04:19 2015 -0800

    lock allocated fabarray pointers.

Src/C_BaseLib/FabArray.H

commit ad4da36b25bc462787ac429353facf8494f24cf9
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:03:06 2015 -0800

    MakeSidecarsSmaller function.

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit 18e046eae8b1e78e860466beda02a01752de0f46
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:02:39 2015 -0800

    multifab movement.

Src/C_AMRLib/StateData.cpp

commit 6dca658885dae1280941be00acd1fb98dfe26d8d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 14 17:01:29 2015 -0800

    lock allocated fabarray pointers.

Src/C_AMRLib/Amr.cpp

commit e131e661dd3f6e781d5327f67c23af98d9b730e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 2b7e5ab74329e92b8599ad2883d07035482680b5
Merge: 6b24b1b 63216b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 14 11:24:19 2015 -0800

    Merge branch 'development' into pgas

commit 63216b5185958fea11b57045edafd625130e37e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 14 11:23:11 2015 -0800

    cleanup

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 6b24b1bb65db6f17a2e7d9231df70f36b2309ccc
Merge: 5c02753 64323b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 64323b528fef5e4a51447916f3dfd58711e4f2bc
Merge: c0ecbb7 f1f1c1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 14 11:45:53 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit c0ecbb794e62f10cc150ee86d85d69dd7947a506
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Dec 14 11:45:44 2015 -0500

    goodbye hopper

Tools/F_mk/GMakeMPI.mak

commit f1f1c1fc265e2ae84af55ee96a87c77ffd8ee004
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 13 16:14:00 2015 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 5802874e8d95f181e440dafc5cf3e04ee13edebb
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Dec 11 08:21:10 2015 -0800

    add gojira and kumonga to DEFAULT_MACHINES

Tools/F_mk/GMakeMPI.mak

commit 9d85114750b4d4627d913c7b35545d647271c350
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9f2371a1ceee34cac93015675bd01d3eb376a625
Merge: 39d7eab 728856b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 17:18:12 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 39d7eab5c1e4e75218fd39a85336d52a181f6457
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 728856b5d5fa97b950bfdae246ccd574f6cd5b56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 88101551401c7dea70ed93d2efdadb4d4e1a2350
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9322fdee92d7b3ac706e4bb2d8574dd559fcc2d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 040a0fa670bc3eab171516c8267a261abcc40dc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b5ed68e848eb3143eee59f4c79679016a4e4f03c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:40:16 2015 -0500

    shut-up the iso_c_binding warning

Tools/C_scripts/moddep.pl

commit 45843b9f0bf70a0cc0708aa489f305a06420e5b3
Merge: d673db2 1a7943b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:26:26 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit d673db246034ebe8e8246737cc1007d37d0f596d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Dec 10 12:26:13 2015 -0500

    homer no longer exists

Tools/C_mk/Make.defs

commit 1a7943baa020860fd4f0e698fc2d1a5c80f20d3e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 cf0767f8bc275cf605d72ed5e0ad9e8d1df2561e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 20:44:32 2015 -0800

    fix typo

Src/C_BaseLib/BoxArray.cpp

commit 95c1040ad0340ddaf12554a00f677c5f05376e42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8866f9e308eca8aa634f622a30ea2214d4baea4d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 9 16:27:27 2015 -0800

    broadcast array function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 09bbf02861bb6b022d957b411c3a0642f12a3dc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2fb17af1cbc970a588988f0fb7012ba01c6a8780
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 10:10:35 2015 -0800

    IndexType: functions testing cell or node given a direction

Src/C_BaseLib/IndexType.H

commit 25e96522aeb44f90c2720321f084af90b9cc4b0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cd001c09c1271824d8ef27cfcbd651e657559f3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5c02753b0ddcfe322174c0808fe3a356d9d3bbc3
Merge: 1e4fc76 8fcf8b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 9 09:39:14 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 2dda63c49e313263f9d0a5ef525590f0cc2b1ed3
Merge: 8a71467 4c52b6f
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Dec 8 21:17:26 2015 -0500

    Merge branch 'development' into openacc

commit f4e684db535db211905da9ae8e0c4322cee6d1dd
Author: vince <vebeckner@lbl.gov>
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 fb73def4ce217b7b1731837cc00b079ffebd0dd8
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 8 16:27:37 2015 -0800

    added virtual destructor.

Src/C_BaseLib/MultiFab.H

commit 7dba73ecd2e43d9b2ab7603062c67c85d17e8763
Author: vince <vebeckner@lbl.gov>
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 74e1dc6c0f004435ab04a58e00282d894445738e
Author: vince <vebeckner@lbl.gov>
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 0003ac35cc9c4ae22f5eb84b3cb422f2687c7599
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 4c52b6f4a15fffe87da98c9dc2be098156714d23
Merge: b76e7c4 fed05e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Dec 8 12:55:40 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b76e7c418f3d350c99bf9dc3e5604bc1c1171192
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Dec 8 12:55:23 2015 -0500

    fix the flags for .F90 preprocessing with Linux

Tools/C_mk/Make.Linux

commit 443270eb6544adf406802f1f15c72ae5b728c4aa
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 18:28:52 2015 -0800

    added undefined strategy.

Src/C_BaseLib/DistributionMapping.H

commit 8ebb6e8b0ba6a8ea9d8e6f28bde546f5182792b6
Author: vince <vebeckner@lbl.gov>
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 d7b62bd70f821b1aa278e3ed77e6390959aa0e90
Author: vince <vebeckner@lbl.gov>
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 fed05e06d02634ac5c7f83d398c9a1a09a89172b
Merge: 88d419a dfbe905
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 7 14:11:29 2015 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 88d419ae1611001a51d6155d256798654bab81c3
Author: vince <vebeckner@lbl.gov>
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 dfbe9051705f0796e4f1cf819185ebb7ddd01cf3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0996ad9e94a2139ef6469cb14d6704ec77409928
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eca8833d3e881fbdd356281adc55a7c6853d19a3
Author: Gunther H. Weber <GHWeber@lbl.gov>
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 c3508fffad9c0910a83b7cb682afd9fdc58208aa
Author: Gunther H. Weber <GHWeber@lbl.gov>
Date:   Wed Dec 2 17:05:15 2015 -0800

    Added BL_CXX11.H to CMakeList.txt

Src/C_BaseLib/CMakeLists.txt

commit 3f67cad9640c6988df1b05c38d93b497230f8d98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:33:06 2015 -0800

    Copy Cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 17790435eb668aba3501988d7b21c11eedc3b176
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:15:09 2015 -0800

    tidy

Src/C_BaseLib/FabArray.H

commit 92fafe604c2624223bbdf5720c89efb52feb8ebd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 14:04:06 2015 -0800

    Fill Boundary Cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 8bc7c1c75dd2a96a862327aeedba653cf9f26452
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 2 13:08:28 2015 -0800

    rework on cache stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4b581880e4f48336ca0653d863aa6bfa0c0b2154
Author: Marc Day <MSDay@lbl.gov>
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 fc393a9720d98767451af84014488cf20f122737
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Dec 2 13:19:51 2015 -0500

    hack in support for branches for the extra build directories

Tools/RegressionTesting/testnew.py

commit 8fcf8b3614051c403887e8d804e6a80e272f7ff8
Merge: 37489ef 1479ff0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:31:30 2015 -0800

    Merge branch 'development' into pgas

commit 1479ff053addfd80ef0865a51dc7129621301beb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:28:55 2015 -0800

    TileArrayCache: improve print()

Src/C_BaseLib/FabArray.H

commit 37489ef6ba330953264d2236cef50efcd3cd6cd8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 21:28:55 2015 -0800

    TileArrayCache: improve print()

Src/C_BaseLib/FabArray.H

commit d7aaeb83fdc52e1a7a95745d05c75c2a104c6e78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9cdd3ca476471059d6226e39f0cde65e255d950d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:50:11 2015 -0800

    MFGhostIter: need to set various indices

Src/C_BaseLib/FabArray.cpp

commit 9bea9bc719dbd394a079a8cdb65d834e639764d1
Merge: 29bc631 115dd3c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:45:47 2015 -0800

    Merge branch 'development' into pgas

commit 115dd3ce46c33d2c40d2bd560e96e3fb983db883
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 20:45:07 2015 -0800

    TileArrayCache: tidy

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 4d6ae524ec25c66f06510338a9074584a28dfd0f
Merge: a8da7a1 c97e7da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:56:06 2015 -0800

    Merge branch 'tilearraycache' into development

commit 1e4fc765f932ecd7393ea711aa5a9be9119cefb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:18:20 2015 -0800

    PGAS_SMC: change defaults

MiniApps/PGAS_SMC/SMC.cpp

commit 29bc631cdcc73038de529e1f093d4ec51cc5d609
Merge: 894ec84 c97e7da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:06:40 2015 -0800

    Merge branch 'tilearraycache' into pgas

commit c97e7dad46f94747db894cc9718b5e90859c9199
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 894ec84773f16c6cbf1621abc4c4e5b9dc0e4616
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 17:03:24 2015 -0800

    fixed MFGhostIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 03976e1ff583c8d01ab2fd8ae41f205886bb826d
Merge: 033b7c7 b8c7b54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b8c7b54660a837dd19bfbb08bc32de548f359f1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 16:21:54 2015 -0800

    tidy

Src/C_BaseLib/FabArray.H

commit 3aed4595fc82baaa9eba906e6237351a4fabecd4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 15:09:28 2015 -0800

    FabArray: stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit ed2b3865e25aaa7b775986e972cdc9aa307f8912
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 14:40:54 2015 -0800

    TileArray: add stats

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 61e671722dcef20142ebc6a34ec352ac839850e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7d41c0305330497e913c746c7fed6ad6ed81dd57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:42:51 2015 -0800

    add MFIter dtor

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit c2bff24c65d89cf536c45073d1185d972276208a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 1 10:40:53 2015 -0800

    cleanup

Src/C_BaseLib/FabArray.cpp

commit 6ed7000adf0a5926ff29d106c54aa471ef40182f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cb148f55963a5c5b6a4dca86bdef2cb581b2a58f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a8da7a1303206af09d002b6c3c763321658c1ea9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f828fb6139d7feefb1093efaa188ad01b112196
Author: Brian Friesen <bfriesen@lbl.gov>
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 666a52fb5d506775cfe03acd4dfd8b65cd800111
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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
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 1424ba4c583ff0fcd84019459b22f96776f83bc3
Author: Brian Friesen <bfriesen@lbl.gov>
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 06ec6a3b1125a94a890ddc6d73bbe970a512430a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 92c64a6a751007a34f9c979b9c4159df707322c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 033b7c71c9c4f3fbf3ed36a52d2a00a11efebedb
Merge: 32b6c95 d82e900
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 da0053a9100b71ab5425d620f55bfe8611014e7b
Author: Brian Friesen <bfriesen@lbl.gov>
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 f1fcd4098ee923afd2f6aab813e548102fe5f70c
Author: Brian Friesen <bfriesen@lbl.gov>
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 1b8df2f9ef94af811f01b8d288abcb8f3974bd55
Author: Brian Friesen <bfriesen@lbl.gov>
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 89a51fd3987c93e6e7b5e5fde7e4c7b3ed6d0e0b
Author: Ann Almgren <asalmgren@lbl.gov>
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 cd89721d766d0b35d667536555356df72f3d6374
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:29:55 2015 -0800

    Typo in comment.

Tutorials/MultiGrid_C/RHS_3D.F

commit ae5c016c949d61ba367e6694b998b8759950a88b
Author: Ann Almgren <asalmgren@lbl.gov>
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 99f3ad5c6c81545c458968e2b03638c439a82010
Merge: a390f99 a7f095e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:29:13 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit a390f99f187e50e9b1158f5a4250f2a3edd19b19
Author: Ann Almgren <asalmgren@lbl.gov>
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 d82e900c1a5e224ce78b7a174afc0f19a965d124
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 13:26:49 2015 -0800

    TileArray: fix typo

Src/C_BaseLib/FabArray.cpp

commit a7f095e84481d1d8dbb864dae19aa13d4f5c1184
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6d8fb99a0b7b1366f6982f549492dd58f54b9618
Merge: 253f585 2822523
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 30 13:07:38 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 253f5852086b05b3714431bbc0f76c14bc0dbd45
Author: Ann Almgren <asalmgren@lbl.gov>
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 28225239dc461e8ae014cd7d809505e6d9b167fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 45ad1bf97c3b9e323e3c6d727b169b58ca1da09d
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 f124691cbd68fd01613fa68889adf84122ec18c4
Merge: 818e5af 45046f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 30 11:24:10 2015 -0800

    Merge branch 'development' into tilearraycache

commit 45046f4a48ca0dbacc3647c98991598ebbfd0aee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 818e5af569dce274473dc17fa63217822ad3474b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b94f324ef97a96efe176559e0d8c1d29951af31e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e0e06ebce42a1e42a96790f3233056f812599b23
Merge: 279f67d e5d0548
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:26:07 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 279f67df3398320bd5ee2c7aa8b7852692f89c83
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:25:49 2015 -0800

    See previous comments.

Tutorials/MultiGrid_C/inputs

commit d691c36713601e292efcf18eb03c4c3a3bf6ac7d
Author: Ann Almgren <asalmgren@lbl.gov>
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.3d
Tutorials/MultiGrid_C/inputs.f90.3d

commit 03535ca0caf9f213928d8a2ff33274cfc2fd65be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 29 17:23:53 2015 -0800

    Have the default be not to test HPGMG.

Tutorials/MultiGrid_C/GNUmakefile

commit 813e6b47a275975fe9f3def3b25b8bc269a06593
Author: Ann Almgren <asalmgren@lbl.gov>
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 b73528734f2d58131dda416b2bf5606dbd7b8c75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 29 07:57:42 2015 -0800

    DistributionMapping: ID

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 9c36beab1b755fd1cf01015418dd48f53df7e65c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 29 07:50:40 2015 -0800

    BoxArray: ID

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 32b6c95fe49dc109c50cbcf0d433af696314c2b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 20:12:00 2015 -0800

    PGAS_SMC: tiling

MiniApps/PGAS_SMC/SMC_advance.cpp

commit 82050fb9928f399392d6dbf4a30ab8183df5553b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 20:11:43 2015 -0800

    MFGhostIter: update for UPC++

Src/C_BaseLib/FabArray.cpp

commit 1d4ea36ebaa33e59ec2993302958feb339b973b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 27 15:14:05 2015 -0800

    PGAS_SMC: change default

MiniApps/PGAS_SMC/SMC.cpp

commit de001b87338894996a2e4096e0337e156574cccb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1a65db7013e0108719c4ee6d6a0b80a9844ed2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77765edebbf098fb50295cf6f3f880d70dc14c4d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e5d0548bbdfdca1aabd729f786b154f9c6340ce8
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 34b8a5fcce04987c2fb91ace022f234cfb5184ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7f63169c1bacec4d8eb2851c2830361ed613164f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cb4276ad3f6b7fff3e1a82c2e6f8908044b7fc4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 377931fea7f9efbe4bf8f0fecb06c023631a0721
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 16:15:14 2015 -0800

    added override

Src/C_BaseLib/UArena.H

commit 30ccf766f3f4604b715b6ed9aae23eaa4be5f41d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 96655578c9712f64c9e90dbfc61d5f6e35a2383c
Merge: e536925 62d03f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 13:47:31 2015 -0800

    Merge branch 'development' into pgas
    
    Conflicts:
    	Src/C_BaseLib/Make.package

commit e53692594c77a3090ba0586aa23087805068eba2
Merge: 017ec59 5e57dfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 24 13:44:23 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 62d03f5ac12df1fbc259deff9f1c650c056ba062
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 de0442caebff1eddf1909419656ed8b8e9ffce33
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fb619d6d01f3ff56adeb7f98f951edfe84c86443
Merge: b51193d 5f927d9
Author: Brian Friesen <bfriesen@lbl.gov>
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 5f927d922ae32834f0804429e5de621a88b1ef4a
Author: Brian Friesen <bfriesen@lbl.gov>
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 17b9e0d5bc05af4c54a6ca64d477e5bdee16c5d4
Author: Brian Friesen <bfriesen@lbl.gov>
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 5f46cbc97555347df8021a5dde2ab70918022699
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Nov 19 09:21:03 2015 -0800

    MultiFab, HPGMG: fix weird comment text alignment

Src/C_BaseLib/MultiFab.cpp

commit 24a7aa8b1a36616f44f25870baf1a4a6a346baa5
Author: Brian Friesen <bfriesen@lbl.gov>
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 59a6c55a2c198765084bd6ed9bd5f652ed936cba
Author: Brian Friesen <bfriesen@lbl.gov>
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 12f366dafedd38069b64766aea27c3aeeee87028
Author: Brian Friesen <bfriesen@lbl.gov>
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 b51193da11e2ab16fee9b49e8fb1effd6de0bf3e
Author: Brian Friesen <bfriesen@lbl.gov>
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 c206e5f5d403847e7c8844b106c6efb55dc5cd88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5a1878a789fdb19fa310b2242880c9cd6f1c0e5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 15:52:17 2015 -0800

    omp clean up

Src/F_BaseLib/multifab_f.f90

commit 1efe8d4a840d007409dc676873c70c14c40b33ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 32ea7b39f4d011848834956aca2f212d02c736c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 12f609ca4691ad9cd331c5ba866f2158f3a4c94a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 11:12:15 2015 -0800

    replaced omp critical with omp atomic

Src/F_BaseLib/bl_mem_stat.f90

commit c975328162185b393fd8cb8081de85de00457dfa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 23 10:49:25 2015 -0800

    replaced an omp critical with omp atomic

Src/C_BaseLib/Particles.cpp

commit 2efd228e9c6460b45acfa527b5fbb1e23bb4bcb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 20 06:01:48 2015 -0800

    Revert "bndry_reg: save have_periodic_bloxes when doing rr_build"
    
    This reverts commit 61cc7595c058eb9d843342ab54d0746ea727cecc.

Src/F_BaseLib/bndry_reg.f90

commit 61cc7595c058eb9d843342ab54d0746ea727cecc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eef0431bb956a6b8f6e01be08643d6ea8a150c26
Author: vince <vebeckner@lbl.gov>
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 3e1d4d261787b93e9b589f2ce083bcb4e2079549
Author: vince <vebeckner@lbl.gov>
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 d99c6fb6c25dd7f0fe0f12051916a434062ae6ba
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 18:26:43 2015 -0800

    vectSize function.

Src/C_AMRLib/BCRec.H

commit e05c8a48961f402d4c42312ce78778ab52278128
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6c81d31623800dd3bd0691794e6aea6ff4f3eb99
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 14:31:38 2015 -0800

    added virtual.

Src/C_AMRLib/AmrLevel.H

commit 23eed125dada541d6bad7f0b8f98f11454132ee7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 18 14:31:12 2015 -0800

    duplicate the initial comm in case it is world.

Src/C_BaseLib/ParallelDescriptor.cpp

commit f053b8c603acb2b09f361e3dccd0c15479015ed1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bee502dc569fab9a865aa4feedb281f907dc8301
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 54c67e68fc700a04c3fd0ca6c859ccef73a46601
Merge: 65f1a67 606c15b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 17 20:54:10 2015 -0500

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ba7def0ca5a3bfa3315786d012da73c0574e3c3c
Author: vince <vebeckner@lbl.gov>
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 65f1a6766a259e9f7e01725554de2a53cd3446f3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Nov 17 20:28:45 2015 -0500

    clean up the parsing

Tools/RegressionTesting/testnew.py

commit 606c15b271f7f8005efe3d743b5fbc104764d12b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 de6ff6e3e94b9c226cbfd91a612cc473716b8bcc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 17 15:34:47 2015 -0800

    AMR_Adv_F: fixed omp

Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90

commit 706676a683c1a0abf4a9d6be5d5119c92d6a8e62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c1299ddb61118b3376ef9f02a438e1497d7a4ddb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a9b927bea25d4cf4d21bce1e70a0179cf7d77068
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3651b11aa31e86d51e4ddb69f6d687884bc7d1e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 777b9169a16e9dd5fbd829d3515aef4bcf0bb0ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9e6f62995ecdfa62ce481c76d7447e600a63670a
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 17 13:00:25 2015 -0800

    cleanup temporary arrays

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit d00a3bc0f7d00efa688144f0b7e11cb751a65bad
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 00883a11d97683bf3094fca3b4e2d77965ec27e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ce988a4f6c662d7512f2f829887911c41e8ac204
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 01b01122c1f343288a8a642e7d65c4a54193f029
Author: Ann Almgren <asalmgren@lbl.gov>
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 a7b00bb61c0b769a7b90bdecbfa5f94e3f1d76af
Merge: eee1a59 b5cdce2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 17 10:15:12 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit b5cdce2eaf072b98ad0502734b3963ed35499f35
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 96a4ee7c702c733d2c2b7a3cf6579e3ccdaa0ba7
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 eee1a59f3eef65aa214863efe7efe63c90d932e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:45:23 2015 -0800

    Fix this GNUmakefile

Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile

commit fc45de027649e21cde40b81072617d2edee0fef8
Author: Ann Almgren <asalmgren@lbl.gov>
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/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/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 cf10ce5d2caa1f200d1c29897d4bf0fccd830c8c
Merge: ae0e2bb 8ca4cb7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 18:10:23 2015 -0800

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit ae0e2bb5cb8d33e4b5722b6c7c7ded98876f4ca7
Author: Ann Almgren <asalmgren@lbl.gov>
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/GNUmakefile
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/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_velocity.f90
Tutorials/AMR_Adv_F/Source/init_phi.f90
Tutorials/AMR_Adv_F/Source/main.f90
Tutorials/AMR_Adv_F/Source/slope.f90

commit 803a5d21d934962147b7090f831dfce593c4ade5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 16 17:42:18 2015 -0800

    consolidate geometry broadcast functions.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit a2b0a281763a7ecb99747eac100426a6b3436481
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 16 17:41:14 2015 -0800

    consolidate geometry broadcast functions.

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 8ca4cb74ade9a3e467dff2c4a52ceb897bfec4e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 89289210310deffd77dfce5d75657b5283c78fb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d23af632bc6a6a9bebada61699bbd615234fefb3
Merge: c6c2111 e9790df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 16:43:04 2015 -0800

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit e9790dfe0f785558a8c7110940489f5ed47a2fe3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 16 16:34:56 2015 -0800

    Update the README_F to correctly describe AMR_Adv_F

Tutorials/README_F

commit c9b7ac79567afa76a60780321c8d0cd1ad539967
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 897687c57b9857e1c7ed4d41d67ba7af6262587f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 c6c211111812c0e80b4d621608d4490534efa9b3
Merge: 2493e9f b525768
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 16 13:43:44 2015 -0800

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit b525768a095bb9985a518aba30ff5e1846b9df2d
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 08db0227fa2fd695d98d9d8dacf34ed744b97fed
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 12:49:43 2015 -0800

    get compute_flux compiling again

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit 4b72890f887a69756f48142934f13c43582770a0
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 2493e9f6df45a61121d86cb119ac47f8fde7982e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8c5f56af469e69fe4d4d14e4db4e22c991a80ec8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:26:44 2015 -0800

    start 3d flux routine - WIP

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit c98c47f24463289ce09ed15ab580fc5797370024
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 11:26:33 2015 -0800

    3d init match 2d init

Tutorials/AMR_Adv_F/Source/init_phi.f90

commit 35d2f46478b12f316cb11e8d530f5dc83860591f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 e4aa9d0c99a8f25be9fe033199a41fa2b1afba1b
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 76b19d2f6f15a6c4031fed4ed6cbe1fcd0c78586
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 00e30df5c895444605fb2814283813ed11ae368b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 10:36:20 2015 -0800

    fixed hdtdx scalining / units bug

Tutorials/AMR_Adv_F/Source/compute_flux.f90

commit acd5c7399e12250e2977b52046437bba7dfa55a2
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 6c6cbf38d0027c75d2b6aa64486b263eee3e9af5
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 9807c469d6160c980a94473907fd6528d72d7177
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 266f8d4d19599825e7589faf0e024166214c5843
Merge: 3ff9fef 3a3b55d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 16 07:35:04 2015 -0800

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 3a3b55d1fc7d21fc2a8d722c24f99b0ab0ee2be0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ff88ca83fdc0db93d1d7a0962b759118860bfe36
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 11:37:00 2015 -0800

    AMR_Adv_C: minor

Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs

commit 08d7d2e4abc614084a3db3e4c48eedf71cac8efd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cb2785d6895142e87ba2ddd8de74f43d8b9822e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f06481684b8ea947b1416fb383ed5115c7fad80a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8971c71508c3c1131a5bd07e709dd354a2293ae7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df7fae96879a2abc930bb379e4c1b9768d6e7837
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 140d802caf800956d58856c8a474e1c01c115b26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9e120a49dee84fa04a7932ae2e07f16bd000365
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 15 10:20:28 2015 -0800

    AMR_Adv_C: minor

Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90

commit 39572883158ce4e0b82ac88160d6d3c500a13a5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 af8667aeff89b2a7c38da51015697496fbc692f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a80d4c9fc42b95e773acd13e1d9090246d2ec237
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/edge_velocity_2d.f90
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 7a7c22dddcb4953ddf7b8c8aae90d18f882df630
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ab7fe7d23a571e8a92cdbde12853bfae21fca01d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5473a3cc399a1ea54daf9c09daf1d2070570f4e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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/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/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 8b0058d58962b4da7b7a26c74454df7d3e5aa9ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8da06a9533e91e435e3dfe9c971051037099678b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3ac90bec61e4f36feaf31e9d03d59346d10e98fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3ff9fef0999c53abb85cee371368ba9b98aba6ed
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 8100d3ab7cab4b9ec5fb00755feb3e94bc119791
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 52b54252b24f1d9065e50543fb3902213adb8289
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 672c81e4ae0b8e5afd444938b407c13bf79c9d7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3a78af91b50146af35e9a6e69f075b6185e109b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 16:44:23 2015 -0800

    AMR_Adv_C: fixed 2d initdata

Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90

commit 9b5e9072f860985471c7151e255eded9d04bab03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77e9042d7bfaf585341cd29767ccc1bba0d43e6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ba538e111bea66fa260eef8a8ab545f5243ff19b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 552e562ac048f5810a3464a3669d878eb6ac18f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:24:12 2015 -0800

    AMR_Adv_C: ADR --> Adv

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_error.cpp
Tutorials/AMR_Adv_C/Source/ADR_nd.f90
Tutorials/AMR_Adv_C/Source/ADR_setup.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_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 09375d61de6cf8bfb4b5a1154f8da90761cd8083
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 04d47bd18c3103e957344bdb9f9b69db14fd091a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:09:46 2015 -0800

    AMR_Adv_C: updated README

Tutorials/AMR_Adv_C/README

commit 2d55fb0dde98b0972a3564b44ca557dcd328aa5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 13 11:09:30 2015 -0800

    AMR_Adv_C: renamed file

Tutorials/AMR_Adv_C/Exec/Make.ADR
Tutorials/AMR_Adv_C/Exec/Make.Adv

commit baf73ae135e851680c9108207235102b1520b5c4
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 d439d15412333bb7d882614dd6519f8229b27246
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 dcb3828f88966566a1c4c321d3e8f5a0d6a7eef1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 e8ab7030074a39ca2c5802c3de61c17ee1ce6fc8
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 d38920a6491860feaa7c07488e7172de45a87a77
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 13 11:11:57 2015 -0800

    remove redundant inputs file

Tutorials/AMR_Adv_F/Exec/inputs-rt

commit de9a7f5fdf546aac98d5750b048a77e3b53c600d
Author: Andy Nonaka <AJNonaka@lbl.gov>
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/GNUmakefile
Tutorials/AMR_Adv_F/GPackage.mak
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
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

commit c037514f59a4414da560f7ad3d3d033e0518f37c
Author: Andy Nonaka <AJNonaka@lbl.gov>
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_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
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/slope.f90
Tutorials/AMR_Adv_Diff_F/update_phi.f90
Tutorials/AMR_Adv_Diff_F/write_plotfile.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 717c9c8c79235586d4f4290859dffa81a98a3102
Author: Ann Almgren <asalmgren@lbl.gov>
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 353751f5973ad155fa65072385ea38d420d0ae99
Author: vince <vebeckner@lbl.gov>
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 47d26e5160c67c4e8f202c3d53a4b813387ff2d7
Author: vince <vebeckner@lbl.gov>
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 d442bace971fee8a131aa3fb998e184fab6d3493
Author: vince <vebeckner@lbl.gov>
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 95f776191aaf7d7ba40492975f3058f9f9400da2
Author: vince <vebeckner@lbl.gov>
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 5e57dfb4e8f72824ce348dd6ef90312d363f1923
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 12 16:04:58 2015 -0800

    added a barrier after we finish advance

Tutorials/PGAS_HEAT/main.cpp

commit 0e701c1891b5ff88e2afea60cb22dd851092a121
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 12 11:16:44 2015 -0800

    added switch default.

Src/C_BaseLib/CoordSys.cpp

commit 68c4c23a45e3f3fdc2cabdc286de22547001e3d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 12 11:16:20 2015 -0800

    added more barriers when we switch between MPI and UPC++

Tests/FillBoundaryComparison/main.cpp

commit 0d15d9e26648f472b43c21e90f36b36864057579
Merge: 4b11934 84b9edc
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Nov 12 07:58:44 2015 -0800

    Add a barrier before switching from UPC++ to MPI

commit 017ec5969d95594d4943d06d90dc83cbe8941be8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 07598fefc221b1a8bdbe135ad5bcb027b938ab6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0a3506f30fd7327cf60155e10386daf9052f0779
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 84b9edc82ee21799f368536c3aae09bee6dba77b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:45:05 2015 -0800

    MFIter: fixed the no sharing flag

Src/C_BaseLib/FabArray.cpp

commit 0e7c7b6643a3f9ea6b3a3d3aba887390f5ebcc27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:42:27 2015 -0800

    auto: fixed Intel complaints

Src/C_BaseLib/FabArray.H

commit ca4ecf8b09924de6a632d3adb43ff884cca0c6b0
Merge: 0cf8cc0 2e819ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:32:16 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 2e819baeead9f49a151a7c13e6e2497b90af9274
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 14:28:40 2015 -0800

    UArena: check nullptr

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/UArena.cpp

commit 42fef258514e1105b319ceac9c84a48b7a90e151
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d625ffee3d67c56bb36f884b7ff0345ed45cb8a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 128a2fbb1a289311b25227bd50e8b0f37dd32394
Author: Brian Friesen <bfriesen@lbl.gov>
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 7c45cf970bdf367695600bc4230120f614e9d7fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 26d1cf30725468a9d1a581e778069e676d093f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dbcc00a8c8cc8d2a63b3cd54442b10f7c7c2bbf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 11:08:51 2015 -0800

    DistributionMapping: use team_for

Src/C_BaseLib/DistributionMapping.cpp

commit c3d72fceac8b4eb33ff1e6a6f1bcbbb52dfe43fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 11:08:11 2015 -0800

    ParallelDescriptor: another type of team_for

Src/C_BaseLib/ParallelDescriptor.H

commit 77efd209b14486e761108771f6ac6e24d83ed1f6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 10:49:17 2015 -0800

    BLPgas: renamed DEBUG to UPCXX_DEBUG

Src/C_BaseLib/BLPgas.cpp

commit bc0e437e3094fcdaac770c71ef4f5a92fd63635c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 10 10:48:29 2015 -0800

    ParallelDescriptor: added team_range and team_for

Src/C_BaseLib/ParallelDescriptor.H

commit de9cab58a20fb829bf8cc775c293ed5bc425b084
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 9 16:45:54 2015 -0800

    low memory option for writing particles.

Src/C_BaseLib/Particles.H

commit 442e5bb044068f5ecdc2b4f51d8a78349ca2ff5d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 15:06:50 2015 -0800

    PGAS_HEAT: added a number of barriers

Tutorials/PGAS_HEAT/main.cpp

commit a8a430d5680d6fcf743f124c12c0df36b72f80ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 15:05:58 2015 -0800

    added UPC++ team barrier.

Src/C_BaseLib/ParallelDescriptor.H

commit 8eb28b7e4b4ce83f370a4d4ef98182b39dabe47e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 9 13:20:06 2015 -0800

    updated VisMF::Write for UPC++ team

Src/C_BaseLib/VisMF.cpp

commit 347eb422570277462e21dee181e415122d169d9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 18fc26054a5b1c2db38ff1fb643a315b8ed8a608
Author: Brian Friesen <bfriesen@lbl.gov>
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 c3192177c699e64335e9160742478f3fb9527373
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d4a37953a6b5297b820c04c6abbf4b0ac0fb5abe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 41794665b0c2cfde6dfb2b146aba71b9576066c1
Merge: ea4ff7f 4c7f765
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 7 10:05:35 2015 -0800

    Merge branch 'development' into pgas

commit 4c7f765839cdc5ecd464a84b6c026cc272cdb801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ea4ff7fff123476732ba3acd19691a85bf493fbc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 6 20:24:10 2015 -0800

    added fab ownership

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/FabArray.H

commit 27f7a8720ffb5fbe36fcb2cb26594cd795437d2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 713463616c77ca9c05b7d0739679ad240f44c7e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dd1103ba90ae8fac8b754e91ab0028946d4164f2
Author: vince <vebeckner@lbl.gov>
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 32db1dea91771506083576522cf58bfd4e3ad820
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:01:53 2015 -0800

    check for correct array size.

Src/C_BaseLib/Box.cpp

commit 4358286bfae8da31dedf7fa652e75e800a81aa21
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 6 16:01:12 2015 -0800

    fixed comment.

Src/C_BaseLib/FabArray.H

commit 62d0e51bb15519758c700e15e64c269fde7a4236
Author: vince <vebeckner@lbl.gov>
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 16730ccf6eb417023c826ba45b0c0403cd8118e8
Author: Ann Almgren <asalmgren@lbl.gov>
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 4b1193413e03149942e9afd1dcacdbd504544722
Merge: 637f78d c30391f
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Nov 6 09:56:17 2015 -0800

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit a1ea949e2b611f569da4f41aebcfaaa396842776
Author: Ann Almgren <asalmgren@lbl.gov>
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 66974912ad6fdbdc4961852fc6bb0b0aa354de54
Author: Ann Almgren <asalmgren@lbl.gov>
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 1304aa28eac4c7c3a004258f2f278a56c1e8fca4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a6c77b2e851e4848016bf162cec5534be42ea35b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 5 16:03:51 2015 -0800

    parmparse setting for particles.particles_nfiles.

Src/C_BaseLib/Particles.H

commit c30391f34d25446297c8b38efc9079f75ec58ad0
Merge: a25f53e 67b3e40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 67b3e4018e4726e752171a48216efe3355364710
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d14dce0f027582711668041aeb40f214fd29c5cd
Merge: 25c02d3 60ddc96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 5 09:51:16 2015 -0800

    Merge branch 'development' into new_particle

commit 25c02d3f5c406dd0d9bce2e87a7351372430b2c7
Author: Ann Almgren <asalmgren@lbl.gov>
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 e76280996f6f4496ee55129ee23554d31137eef4
Author: Ann Almgren <asalmgren@lbl.gov>
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 a4842f6123e69a1817cef2e3d397d2c4abf68700
Author: vince <vebeckner@lbl.gov>
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 b14be1b43c2d33e7ef5324d9154c7da43d2f2c92
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 4 14:53:36 2015 -0800

    proc numbers for all.

Src/C_BaseLib/ParallelDescriptor.H

commit 1393ed6b06df5e9d59a70f1922919028979644f6
Author: vince <vebeckner@lbl.gov>
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 0e5d34d491e09332371bd9b2b94f8c8a9cb4648a
Author: vince <vebeckner@lbl.gov>
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 6afa709c4b6886ba739b6ed2c92bf46f387eb3d5
Author: vince <vebeckner@lbl.gov>
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 45a8717e4168bc14959fb469bacb15765432286a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 3 15:34:02 2015 -0800

    added a few diagnostics for dynamic sidecar development.

Src/C_BaseLib/FabArray.H

commit 60ddc9634c6e46d306fe71ed53b461a462e5acaf
Merge: c88bdc1 d93465e
Author: Regression Tester <ccse.lbl@gmail.com>
Date:   Tue Nov 3 12:21:16 2015 -0800

    Merge branch 'master' into development

commit c88bdc1142bbae8dba20e2f48da50fb37bd6f45a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1d2f04f10e661ee4608f1aa72c01d606ffdc9bad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3f418c12d625963f593301d9d10cdd25d9abfb7e
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:46 2015 -0800

    Revert "IntVect: move static variables returned by TheDimensionVector() to anonymous namespace"
    
    This reverts commit 77fdfa30c71e47db82c9e951e5fac1ee290beb28.

Src/C_BaseLib/IntVect.cpp

commit 249f3794da74f8fd289131a5dc1d96f50172be62
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:45 2015 -0800

    Revert "IntVect: move all remaining static variable declarations to anonymous namespace"
    
    This reverts commit 90526ea2379029f87e03ec15a5410711be296878.

Src/C_BaseLib/IntVect.cpp

commit 7d0f0d3ddbdc297cf22799f02ba2d915c4aafef2
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:44 2015 -0800

    Revert "Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace"
    
    This reverts commit 22722204fe5ec61e5a9a7b884eec3e098c8309f6.

Src/C_BaseLib/Box.cpp

commit 27821bce94cc9e2099f2d06cf3417ccdac9c5867
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Mon Nov 2 15:27:41 2015 -0800

    Revert "IndexType: move static variables "Cell" and "Node" to anonymous namespace"
    
    This reverts commit b46bb53e161a418d6f14d5b6ab00a6224798a939.

Src/C_BaseLib/IndexType.cpp

commit b46bb53e161a418d6f14d5b6ab00a6224798a939
Author: Brian Friesen <bfriesen@lbl.gov>
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 22722204fe5ec61e5a9a7b884eec3e098c8309f6
Author: Brian Friesen <bfriesen@lbl.gov>
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 90526ea2379029f87e03ec15a5410711be296878
Author: Brian Friesen <bfriesen@lbl.gov>
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 77fdfa30c71e47db82c9e951e5fac1ee290beb28
Author: Brian Friesen <bfriesen@lbl.gov>
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 341767153c9bbaf3fc17510086700ff29fdf956c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 14:41:21 2015 -0800

    MultiFabUtil: fixed bug in my last commit

Src/C_BaseLib/MultiFabUtil.cpp

commit 49cb0ad04d137c5c69a1f9e2e1ca6e4f535ce3d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ff9b0150d5f81b4103122d93e15a0666c562128c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 2 11:27:26 2015 -0800

    MultiFabUtil: thread safety

Src/C_BaseLib/MultiFabUtil.cpp

commit 405234dc1aa3a74c5a327437d53dd3da6d04fff6
Merge: 42813c7 d28433c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 2 11:25:43 2015 -0800

    Merge branch 'development' into new_particle

commit d52abac80e5e1eb8ee8238a444a3ea982796a382
Merge: 8ccf41e d28433c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 2 14:25:35 2015 -0500

    Merge branch 'development' into plotfile_ghost

commit 8ccf41e12c309cca100c7b668c104c89267ff8bd
Merge: e36f0df 4a062ad
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Nov 2 14:25:05 2015 -0500

    Merge branch 'development' into plotfile_ghost

commit e36f0df5fb7ede7443691aa9aa459fa28cb0789c
Author: Ann Almgren <asalmgren@lbl.gov>
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 d28433c25f0ec2c5eab73debb44050610cc0c960
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d93465e6e0324f52ed87a3c4ec052685f241e2db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4a062adc31d335ba104beb7c01a465faf46dfc7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 1 19:43:14 2015 -0800

    Make: flags for using fsanitizer with gcc

Tools/C_mk/Make.defs

commit 3bd23d536cae2c99b599a570658ee17e037cb870
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 603f0d835b33d2a0976df772c834b82ffc7c7c1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1bfebf668afef8c789518695e9f6a1c61d2d24be
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Nov 1 17:46:02 2015 -0500

    copy the diffDir if we do copy_benchmarks

Tools/RegressionTesting/testnew.py

commit 8cedc1dc3a2159545fb05f8ae56bb577de566e1e
Author: Ann Almgren <asalmgren@lbl.gov>
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 6021957a58bae89efab7acb679601da0d28f8957
Author: Ann Almgren <asalmgren@lbl.gov>
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 28438156b80e8693397855ce9e29ec270d5fc880
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Oct 31 18:39:09 2015 -0400

    lots of compilation fixes

Src/C_BaseLib/MultiFabUtil_1d.f90

commit 66da880452afb80f2c34c0d69eaa7e252f7746cc
Author: Ann Almgren <asalmgren@lbl.gov>
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 4934a856c6cd85d5f118f5cd85d39f2271e20830
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 30 15:16:15 2015 -0700

    MultiFabUtil: fixed function arguments

Src/C_BaseLib/MultiFabUtil.cpp

commit 3fa7c97ede3676eb554292247e98b8b0a8dbe705
Merge: 72f3906 8425b25
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 15:02:21 2015 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 72f39060861444aab887fc41f36bac03fafa441b
Author: Ann Almgren <asalmgren@lbl.gov>
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 8425b25fdce2a8d4ae79be679a780fd3025deb7d
Author: Marc Day <MSDay@lbl.gov>
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 c133a60dca215bbc0e7dbde45883942da3e78aad
Merge: 147850e 520ce78
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 30 13:08:06 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 147850eb97403cec73295015c1a8dac54babd0e1
Author: Marc Day <MSDay@lbl.gov>
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 520ce78a872fe1fc072669a6ab774f39df90eaed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 42813c734cede4c9ab8a96225615346c2d1e3efa
Merge: 114c631 99fa8b5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 30 10:19:11 2015 -0700

    Merge branch 'development' into new_particle

commit 114c6318cc8df9b8c1fdc11f36f75cc4dc105edf
Author: Ann Almgren <asalmgren@lbl.gov>
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 b28ac19101f0b760887502f09b3104cfc160f547
Author: Ann Almgren <asalmgren@lbl.gov>
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 965a43dce9ebe4b3a4fb6a80ed12cfef24056ff8
Author: Ann Almgren <asalmgren@lbl.gov>
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 7b04c5c3eb536b54a4bcfa9e748e2065e18504dd
Merge: 0509a29 bbe84d0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 29 16:52:29 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit 99fa8b5277f77edfa4313488a8f7f98280ede50e
Merge: 45f00af 9fb393e
Author: Changho Kim <changhokim@lbl.gov>
Date:   Thu Oct 29 13:24:32 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 45f00af07f5f88e35d65d98f9be602049ed28b64
Author: Changho Kim <changhokim@lbl.gov>
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 9fb393e0ae6217851fef104793685b166fdbb101
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 16:12:08 2015 -0400

    missing contiue

Tools/RegressionTesting/testnew.py

commit 12e81f889115769169a56997668d87506eadf930
Merge: 26b18fc c5231a2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 15:59:15 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 26b18fc7c559860e3d4afd949b7bdeb6e459b736
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 29 15:59:07 2015 -0400

    fix the output of the diff

Tools/RegressionTesting/testnew.py

commit bbe84d09135f7a724b218ff553848cd8714bca26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 12:58:17 2015 -0700

    PIC tutorial: use FMultiGrid

Tutorials/PIC_C/solve_with_f90.cpp

commit 1094e40892a7b36d9fd0684ad67435406503b157
Merge: af036f3 c5231a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 12:57:25 2015 -0700

    Merge branch 'development' into new_particle

commit c5231a2cc8f391246508419fbccd561f877ec8d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 af036f387a5262ff7bddad89c36374843faffed8
Merge: 3ccf731 039bb0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 29 10:48:32 2015 -0700

    Merge branch 'development' into new_particle
    
    Conflicts:
    	Tutorials/MultiGrid_C/main.cpp

commit e798d71486615f6f4bc4a78731304c8222b87d41
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 304b007051262d19ef87155dfd1146e0efe3a87b
Merge: edcdac7 b3e2fa6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 19:23:07 2015 -0400

    Merge branch 'development' into plotfile_ghost

commit edcdac7eadc5c9562dc8e2c9304d9e56121ad09b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3910470c035cd7a37b8fd4a18fa8e2af42b9d009
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 28 19:00:13 2015 -0400

    this works with ghost cells now

Tools/Postprocessing/F_Src/fcompare.f90

commit 039bb0a6aaa112f9d5fcee44ad41115f3833c433
Merge: 4e433a9 b3e2fa6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 28 14:19:23 2015 -0700

    Merge branch 'development' into ctof

commit 4e433a909738736b5fc3b1f9948d630d3803802e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 83a25bb7f8b2261488207452e2c5ec28ebb9f795
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b3e2fa6fa569efe9eebb803a7c6ffd754068f1ed
Author: Brian Friesen <bfriesen@lbl.gov>
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 e65269c478c2724d5e46d766095d91661acf19fd
Author: Brian Friesen <bfriesen@lbl.gov>
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 de7807387a77eaddb87cff06bf963aca774ec293
Author: Brian Friesen <bfriesen@lbl.gov>
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 322f57749668b6cf84dba2003e78a45872845548
Author: Brian Friesen <bfriesen@lbl.gov>
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 3f16894617e0b3e011cc38d922ecebfaeea24f5c
Author: Brian Friesen <bfriesen@lbl.gov>
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 6730f829ef19b9d8182a798529da6d7e835b8f65
Author: Brian Friesen <bfriesen@lbl.gov>
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 998884b5727fe57abb0318522c34f0013fe50c64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a75c719d1eb17d3ba9254c543dda84711023840e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 27 10:14:01 2015 -0700

    FMultiGRid: added functions for diffusion operator

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H

commit 0509a29ffbf7dd59ee578657871e24cabb845a1d
Merge: ced6c50 2b14f97
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 27 10:09:40 2015 -0700

    Merge branch 'development' into new_particle

commit 2b14f975f1b6fc4a1941183cd92a0e3dcaab093f
Merge: 26ec4a9 8ccd90f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 27 09:45:38 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 26ec4a96770eae545a2fbe5a73f5bbd5905c6baa
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 27 09:45:17 2015 -0700

    added 1d file.  some subroutines now working yet.

Src/Extern/amrdata/FABUTIL_1D.F

commit 8ccd90faa13e00eeb86252d17fb8e120a46aa2e4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b76e83636ad159f3353e2ad84a2ddf58a6240dfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2b9ca32bdb7cf79bef24d96a0983eeda798d605f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 26 17:01:06 2015 -0700

    dont use the word signal.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 3822a65a1df6f8ca3b105f82479fad58285149fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 28ded501cb40d0c11210180ed223865e688857fe
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 26 16:00:10 2015 -0700

    make safer data broadcasts.

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit f73c2dd7cadec0447333f8d89fb5fb886e5c174c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 15:32:31 2015 -0700

    minor cleanup

Src/C_BaseLib/MultiFabUtil.cpp

commit b9c2a185607f2d4f52c43a2b22ecf1ebdaea0138
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 14:09:59 2015 -0700

    MultiGrid Tutorial: use FMultiGrid instead of MGT_Solver directly

Tutorials/MultiGrid_C/main.cpp

commit fe9c19967a416e85b82c78a3e8f9958a5e4ceb89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8aea0c47d757c3acfa5ded8b44c6812cdb7524b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4abd17a413a984b9a1c600d5a26a57baaf3b2982
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1ad11e7486af9f6f5aec8c7d60bc6b339875f663
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e86986663d575dcc4221c8fdf537764840ef2828
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 26 12:40:21 2015 -0700

    MultiGrid Tutorial: removed unnecessary ghost cells

Tutorials/MultiGrid_C/main.cpp

commit addeb91bf6072400345402e039bf51d512f8ed55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ab6cfb90dcb211cd83ab2e59c62e1ab2701cbd82
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 821b1ef3eea51f3c384d706a9623b4f5a97bfcd0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Oct 26 10:47:44 2015 -0400

    fix the build git hash stuff

Tools/C_scripts/makebuildinfo_C.py

commit b455b012b0c9dc7e4535dd7b47e02ee33939d719
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 616b29423217bba0e2be5e5ce8c8b76d3955e2e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 25 16:06:22 2015 -0700

    FMultiGrid: bug fix

Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp

commit 26bc569df18ce3c948516bd937851149c9736bab
Merge: d98a940 3ee6d99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:12:38 2015 -0700

    Merge branch 'development' into mlcc

commit d98a940e2c3075eca9ac367d48425c5e9c9d6a79
Merge: 1179ab8 c37a43d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:11:52 2015 -0700

    Merge branch 'development' into mlcc

commit 1179ab8f6117043315327c27017ad2732097e5de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 22:10:41 2015 -0700

    minor

Src/C_AMRLib/Amr.cpp

commit 2c8cee1528b283856f0e7180a4e503cae4f2b8b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 24 20:42:05 2015 -0700

    fixed comments

Src/LinearSolvers/C_to_F_MG/FMultiGrid.H

commit ff34bb6c78c35e38ef48cb4cd28f3d4bef53346c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4afc30e719e77b61788ca100cfbdf349fbf5d74b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ced6c50c95572b0fd127802bd19ada90f9d40d46
Merge: 3ccf731 3ee6d99
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 23 17:15:53 2015 -0700

    Merge branch 'development' into new_particle

commit 3ee6d99efe7becb16a58488f0ca44a835b760bf1
Author: Ann Almgren <asalmgren@lbl.gov>
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 3ccf73145aa0c37d21b9230ce94b416904aafb6b
Author: Ann Almgren <asalmgren@lbl.gov>
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 092934fcadb1eb0bb5e615acffb37bdea3f55a7a
Author: Ann Almgren <asalmgren@lbl.gov>
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 6b4cbeec4496ceb81c8bbd5a863655eaf8eae0d0
Author: Ann Almgren <asalmgren@lbl.gov>
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 ec0c394836eae13840018bce3ecb0ddab8382ca7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:42:53 2015 -0400

    more safely get the box indicies

Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90

commit 4979330b0a40e684640f8b9a19864e87bb000749
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:33:56 2015 -0400

    eliminate lbound/ubound

Tools/Postprocessing/F_Src/fsnapshot3d.f90

commit 5f44fd5458a40517b3735781ea56800679a75624
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:28:26 2015 -0400

    remove lbound/ubound

Tools/Postprocessing/F_Src/fextract.f90

commit c1339209db580cb6a0e5969dfaf167b7bea0e146
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 23 16:21:16 2015 -0400

    add get_pbox

Src/F_BaseLib/plotfile.f90

commit 9e479ad2a7a446fb413a320a9c661a9e852d624a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 22:13:57 2015 -0700

    Remove excess print statements from Particles.H

Src/C_BaseLib/Particles.H

commit a5fff7240c8d622d4f491805cc42ebe145a37536
Merge: 3d2b665 c37a43d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 22 22:13:36 2015 -0700

    Merge branch 'development' into new_particle

commit 864f35e2a1e008c0a19d6489c9ab4368ad8266f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 22 21:52:32 2015 -0700

    PArray: removed isConstPointer

Src/C_BaseLib/PArray.H

commit c37a43d937df2fe368f42c5963623f1c48fc8a12
Author: Ann Almgren <asalmgren@lbl.gov>
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 3d2b665451bd2f72daa2f5369d900b3ddeed0ffd
Author: Ann Almgren <asalmgren@lbl.gov>
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 50e8315c7e83a90c7990da17c0794cf6fc54292d
Merge: 915a91c a62e608
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Thu Oct 22 19:16:31 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit ecc4133bfb46173c79c7e666877b49b26a5e9f58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 16cd170e4a2c4ab1c35cc1ea0287725748a8e592
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6cff72b6e7bdb92a69141d67a5df07118e215de6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8a714678061d3001253d771653086922c8d39e4c
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Oct 22 15:12:25 2015 -0400

    Add ACC flags to fortran mk

Tools/F_mk/comps/Linux_pgi.mak

commit 5fdf7a40ece9276b4421cbcde997b884434a8191
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Oct 22 15:00:04 2015 -0400

    Start adding ACC to PGI build

Tools/F_mk/comps/Linux_pgi.mak

commit 996ccf938abce78a29190bb2f8a90b0ce32ed886
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:34:05 2015 -0400

    some notes along the way

Tools/Postprocessing/F_Src/TODO_GHOST

commit 60515f35acb851ca305ce2d45a898d49f90d8bcd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 47a837eb1c4c5e2b7489121dcd1c52f82abdb1b8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:09:51 2015 -0400

    remove unused lo and hi

Tools/Postprocessing/F_Src/fcompare.f90

commit 18cfed5b8e7592965ea56bcc9e137ce14a0d07e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 14:06:12 2015 -0400

    use box_equal() to simplify some stuff

Tools/Postprocessing/F_Src/fcompare.f90

commit 0cc0c640d2cd7862a918141fbaa5eb02eaa662d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 13:56:51 2015 -0400

    use volume(get_pbox) in the isnan check

Tools/Postprocessing/F_Src/fcompare.f90

commit 7050823982e559f2bf7562838db08e8e7aa6dc37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 22 13:44:15 2015 -0400

    more work on getting ghostcells into plotfile.f90

Src/F_BaseLib/plotfile.f90

commit a62e608c4ba218e2262117ebafb2909c0ed2e7e2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a47057b6a409fb5b43d8d5697e91b58777ab082c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5880daad4e247b1aec962185fd8a825275756d6f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d30164df1db8e50a1e0e03bc26fb8b9b7e59097f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:58:54 2015 -0700

    Made loop to test multiple sidecar sizes.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit 7f879b02035105f306da0fefae954864198d296f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:34:56 2015 -0700

    Support for dynamic sidecars.

Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit f71ffb22221f96bf9aabad5849f109d01ce24a93
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:23:51 2015 -0700

    resize to zero at the end.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit cafe58c6310dec78287ea45d96388d890ad7487e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 21 17:21:05 2015 -0700

    test with two sizes.

Tutorials/Sidecar_EX1/SidecarResizeTest.cpp

commit 68fe925d79c2b5e2bf826520bea7bc8a069b884a
Author: vince <vebeckner@lbl.gov>
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 fd6d17379041bfd5c75162c095f3efcf0d31c141
Merge: a9812a4 6d12365
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 15:00:18 2015 -0700

    Merge branch 'development' into new_particle

commit 6d12365c7fd86457d0aaee3c6a6c98cc8fe566a2
Merge: 2b0e48f 57ed9f9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 14:58:39 2015 -0700

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 2b0e48f955964e52d13e7715e042fffa8bf9dec8
Author: Ann Almgren <asalmgren@lbl.gov>
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 a9812a49355a59d1629d1e701e3cc79ad2e0a969
Author: Ann Almgren <asalmgren@lbl.gov>
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 915a91c95e360424234a6f4019b13673c0653e16
Merge: 00aae4f 57ed9f9
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 17:23:01 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 57ed9f97445baf9b7e434a423557d1be0f49b619
Author: Brian Friesen <bfriesen@lbl.gov>
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 00aae4f64f6115fc4cd77522fe6bc1f496f95b02
Merge: a3012f4 38a1fff
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 16:05:52 2015 -0400

    Merge branch 'master' into development

commit 11351d0cc0c06b3b3257d2ca46a3d3e59cc0307c
Merge: 9400b54 a3012f4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 13:03:50 2015 -0700

    Merge branch 'development' into new_particle

commit a3012f48794238e9a0ae19a13788eaa97bfe93fc
Author: Ann Almgren <asalmgren@lbl.gov>
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 38a1fff6df105c5b0161bacf2a4e12495ac34fd1
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Wed Oct 21 16:01:34 2015 -0400

    add support for my mac

Tools/F_mk/GMakeMPI.mak

commit 8caf7d247062306b3dee32c1949a2e8b1ff8ba7a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9400b54972512f389cb76308e0d7ddd454192d40
Merge: d6f49e3 b625fe8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 12:55:10 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit d6f49e3d9af107730153d2277ab38d48cf5ae946
Author: Ann Almgren <asalmgren@lbl.gov>
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 b625fe80bc7a6e1e0d6dab9b5b6473a06dfd37f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 094380191ec2e48da65f5e268d8385337ae8ca95
Merge: 1844118 c503147
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 21 10:40:15 2015 -0700

    Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle

commit 184411870398b3491afab6cf90a7cea527c90e87
Author: Ann Almgren <asalmgren@lbl.gov>
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 553a31940291f58f283d21bc46287c1efb1d0382
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 19 11:10:37 2015 -0700

    code cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 4d9ce1c588841e9c2733522e3193464b6db33b82
Author: vince <vebeckner@lbl.gov>
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 ae87803b55ce54c70433b37d24538235cad2fa57
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 16 15:28:52 2015 -0700

    fixed comment.

Src/C_BaseLib/Utility.H

commit a87888a48a2fb064663542058203f145a60fe26f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:51:25 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2b5532dbbd8a2421772af318b738fcb1e0699a84
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:47:55 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.H

commit cf5c3586cf3ec3b189f0e328b62c75dc74448f4b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 13:35:37 2015 -0700

    comments.

Src/C_BaseLib/ParallelDescriptor.cpp

commit c50314788b13c9caef25670b675c003b376acc59
Merge: ae85828 7af747b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 21 10:27:42 2015 -0700

    Merge branch 'development' into new_particle
    
    Conflicts:
    	Src/C_BaseLib/Make.package

commit 7af747b0d67791ba435623db8165c11ea391af65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ae85828cf579692c6114b910f40a5cfe990ae9ab
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9ffb2bf3e9a7c3403ce26d4d194625872508708f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f2562316a806507d2759c5f595ed8b01f3551f7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c7c7e27b23bd3bd67a637fb2d439921964c7a6a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 081b9cae3d63e73519fadb4b84aea0cce8c3870e
Author: Ann Almgren <asalmgren@lbl.gov>
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 9ab6db5a0a41712a5373965c834fd9ab3f1721b1
Author: Changho Kim <changhokim@lbl.gov>
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 ce0800878614b2650fcdd8657e42d05701096f4b
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 1d510d5c6894c0b2aa89485255ea85db4c875e3f
Merge: e3a7e50 844e49f
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Mon Oct 19 13:05:31 2015 -0400

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit e3a7e50bd719571be3fbe4e798f4e83addabad1c
Author: Chris Malone <csep23@chester-login1.ccs.ornl.gov>
Date:   Mon Oct 19 12:57:03 2015 -0400

    add support for fortran chester for development

Tools/F_mk/GMakeMPI.mak

commit 844e49f69c772996f50e8dad4f484e21f8e91fdb
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 5c68a41d2a0322e3af40acc8cfdeeb62974edcb3
Author: Brian Friesen <bfriesen@lbl.gov>
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 1073059e6812f3dcb94646ca12716941292a5af3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 15 16:20:00 2015 -0700

    BACKTRACE: catch SIGTERM

Src/C_BaseLib/BLBackTrace.cpp
Src/C_BaseLib/BoxLib.cpp

commit 0cf8cc0d7c0d626c20ae038cee232a5b8dce47ab
Merge: a25f53e 4a94cce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 15 11:15:03 2015 -0700

    Merge branch 'development' into pgas

commit 4a94cce60d09031e3108a78287e724ef5f101fc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 14 15:13:04 2015 -0700

    added flags for gcc thread sanitizer

Tools/C_mk/Make.defs

commit 8cfce749c7bc6959a00bbcde21c325980eb2f219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5e2e442f647972175ffab4bdda205c066b601381
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 14 14:00:02 2015 -0700

    disable omp in FillPatchIterator::Initialize for some LMC problems

Src/C_AMRLib/AmrLevel.cpp

commit 91000f01bcb008db391d3d6b597d3731ec378d7a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Oct 14 12:27:34 2015 -0700

    Fixed bug in looping for 3D MFTower fortran

Src/C_TowerLib/MFTower_3D.F

commit 6ee18d858883ecf7f0cc1859719cb6044d6f608d
Author: Ann Almgren <asalmgren@lbl.gov>
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 0f7654641f090867ede01bd6c830c6e1d4c7c4d0
Merge: e384305 7d4dadf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 13 13:04:43 2015 -0700

    Merge branch 'new_particle' of https://github.com/BoxLib-Codes/BoxLib into new_particle

commit 7d4dadf0f7db36f445e2888daae1d2f405439eec
Author: Ann Almgren <asalmgren@lbl.gov>
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 e3843053cc30b4205ee11ea303029b822726d13c
Author: Ann Almgren <asalmgren@lbl.gov>
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 af19914ba6545779f5b429cbb7e67920801e26db
Merge: 8b8e213 7b48024
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 13 10:41:37 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit a3357bb5912b85cd69cd7d53ce0bb8ad0ac3ecd7
Author: Ann Almgren <asalmgren@lbl.gov>
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/BCRec.H
Src/C_AMRLib/BCRec.cpp
Src/C_AMRLib/BC_TYPES.H
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 211f414c6ae4859f3d6d8a6ab3e4db7baa4359b4
Merge: 15a51cb 1408ae1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 15a51cbd5031e427106d2274d1648ca720851778
Merge: 9dd6cbd c49ce10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 22:08:58 2015 -0700

    Merge branch 'PIC_Tutorial' into new_particle

commit 1408ae17889d47c51fe3b78011c8b90b8fabf2ea
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 22:06:02 2015 -0700

    Add AssignDensity

Tutorials/PIC_C/main.cpp

commit 9dd6cbd1985d0693843ee8aaef048232e2ad5f4d
Merge: 84aeeae 7b48024
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fd82b7d4eed7da4aeb32aa5af1d6e8fc452ec97f
Author: Ann Almgren <asalmgren@lbl.gov>
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 6842f7320e360c94687555e562ef772f7ea89dc5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 22:00:48 2015 -0700

    Fix for new gdb stuff.

Src/C_BaseLib/Particles.H

commit 84aeeaeac4b66b37bb78b01acacb44bf46db9e15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 20:59:55 2015 -0700

    Particle: forgot a new file

Src/C_BaseLib/ParGDB.H

commit 838e2e7168795cabb58619cb8d52fa5409666ee1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp
Src/C_AMRLib/Particles_1D.F
Src/C_AMRLib/Particles_2D.F
Src/C_AMRLib/Particles_3D.F
Src/C_AMRLib/Particles_F.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 bb0f68db1759fde590b031833f722265946314a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 693e835377985473f3dda99ed04fc63d764c5b55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 afb0ad4bcface9c61fbfc07fd021cfdbd08884a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 19:05:59 2015 -0700

    more on the Amr independent particle

Src/C_AMRLib/ParGDB.H

commit 73e34f7073a9fc6601c652021558fc142dc6766b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 847b7ec65811c7f0408a01abb93d6c8023e9f662
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 11 16:42:59 2015 -0700

    forgor two new files

Src/C_AMRLib/AmrParGDB.H
Src/C_AMRLib/ParGDB.H

commit 205fec1893ea3548b737aee3533343c9dfa67018
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b48024bca216d4267450b4e367b0dd7e46a5f0b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3167ce84c18636aa872fa96408020f2e5504fdb4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c49ce10843b2749ccc67b3d13c2a0b68ca30c764
Merge: d2c99ac 761bce3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:44:46 2015 -0700

    Merge branch 'development' into PIC_Tutorial

commit 761bce39b21cb0d59619f3186c9fb768f118ca9d
Merge: d0e3b80 92bf9c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:22:03 2015 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit d0e3b804c924e3c15d6e9fbf6570dcf5a8588a69
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Oct 11 15:21:47 2015 -0700

    Fix a comment so that it is now correct.

Src/C_AMRLib/AmrLevel.H

commit 92bf9c96cf2f12f552f1f61da49b2b83ce38883c
Author: Brian Friesen <bfriesen@lbl.gov>
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 6e039d40bd26a91c588cb879f739eed8763ced80
Author: Brian Friesen <bfriesen@lbl.gov>
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 b273a163fca2f251e8051d0b7fb1c12280c5b5d0
Author: Brian Friesen <bfriesen@lbl.gov>
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 c669702c513124c31485d89a8df795bb17ce8b3f
Merge: 6d02a72 4563183
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 9 19:39:54 2015 -0700

    Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development

commit 6d02a726c56e33c7bc8e3cd7d4731216ef08f9df
Author: Ann Almgren <asalmgren@lbl.gov>
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 4563183b5ae403c3f92ea9c5eaf4af78c26c7f8f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 66943d493f2d2e182249dc385c53371f19b8bb18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1c9f9e0c24434ac42112a04562fba6c3b2b8e25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 16:18:16 2015 -0700

    BACKTRACE: update Readme

Docs/Readme.backtrace

commit d56377f5c6631b06723cdb0e7ad0c008b5e958a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 15:48:02 2015 -0700

    BACKTRACE: output to files instead stdout and stderr

Src/C_BaseLib/BLBackTrace.cpp

commit dba469396b672a1b141a4d0a6c40a22af9f98e9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 479282f0f3b6f1ae6d41aeec3af8839e72a7d9c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6013d36fb609b6c6a07d96a6acb28909cca81c88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e27bd8e62a616a324818dc644dddd3eb252153f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f88ef33a8ce83eaa0b6e9cdf29557540a011db69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 9 13:44:10 2015 -0700

    fixed a bug

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit d2c99ac7febe76774822a099964059c224ecbe25
Author: Ann Almgren <asalmgren@lbl.gov>
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 1ad6e0879542b92fa4c6b7de7342a2edbefb1629
Merge: 81079ea f277d58
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 9 11:32:59 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 81079ea9df828f503441fb2a92feb1740a583e8e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 9 11:31:21 2015 -0400

    this now works with python3

Tools/F_scripts/makebuildinfo.py

commit f277d58494dbb95d871673c3946a07ae93adf0b5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:33:49 2015 -0400

    more python3 fixes (__cmp__ is replaced by __lt__ for comparing)

Tools/RegressionTesting/testnew.py

commit 38a6da182fbd2c25a431b3f9cb041f4dd8966f4b
Merge: 29d3ffe c94bcff
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 22:22:29 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 29d3ffedb4c9bf126f837809d92b4b8b21e34c7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c94bcffb66fabf320af93808deb85c31c9333f21
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 2f4584817b89173278321fbca00e1087ca75f8ce
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 8 13:45:39 2015 -0700

    fix for 1d amrvis.

Src/Extern/amrdata/AmrData.cpp

commit 2835cc433b812c263fb4dfb6d96b71223189de48
Merge: 53fc7e7 ce9c0e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 8 12:25:05 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 53fc7e7cb0494bcb997c1331277ed3813ec00601
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ce9c0e66c94fdbc5312d2710ec5f563af1c5b52b
Merge: 96078bd 1ef2d56
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 7 15:57:45 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 1ef2d568a1280624e4b63daaa5e3c17220b6ebe1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d28cb983f5ee33565eb888976964d4434759eb29
Author: Ann Almgren <asalmgren@lbl.gov>
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 a25f53e2d8ca3756e04c14bb3d75a73f54ad57fc
Merge: 76f504e f54d01f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 6 14:51:08 2015 -0700

    Merge branch 'development' into pgas

commit 96078bd75b77361deaae57e85c72cb1fdb35dc45
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 5 13:33:16 2015 -0700

    define constant for 1d.

Src/Extern/amrdata/AmrvisConstants.H

commit f54d01f55ede0f5cfd566899a30ed15fa8e50441
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9a8ca200a4ee5d4187ccedd929fa4ef9f0d2df86
Merge: bca8808 80e1f61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 5 08:58:58 2015 -0700

    Merge branch 'poisson' into development

commit bca88084f5e0285b4b1b22d108723da217399f43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Oct 3 11:45:33 2015 -0700

    make BoxArray::boxList possible for return value optimization (RVO)

Src/C_BaseLib/BoxArray.cpp

commit 25c945158e12e37ab6ff93ee5a163237f6893c61
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d1a6539fc485436cd4d3c10c5544d05f6ae83c2d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:50:37 2015 -0700

    quiet compiler warnings.

Src/Extern/amrdata/DataServices.cpp

commit 2d390ce4094770bc297d99bf52c05dd174ca8b13
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:48:14 2015 -0700

    only print for special debug.

Src/C_BaseLib/FabArray.H

commit c50577d1a8ea2c5a97c5cf0a248889867754a96e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 2 16:47:39 2015 -0700

    quiet compiler warnings.

Src/Extern/amrdata/DataServices.cpp

commit 80e1f612f078c1a9d51bf7592ec6436ef8933369
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b08bef8f7c4405b39ec94a522bcf72bba01767bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4d365d3bc1b0032b73b3bdaaacb7229d9532eb42
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 1 18:19:47 2015 -0700

    optimization in stencil_set_bc

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 7a53e757bc3d65da260c360234c766bb11195f86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 160e24dbb0e67e57b9afa196f6a298729361131e
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:12:38 2015 -0700

    cxx11 setting.

Tutorials/MultiFabTests_C/GNUmakefile

commit 96e0c60866ba895f4b92330d70e8cb8909151eb3
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:10:41 2015 -0700

    added profiling to tFB.

Tests/C_BaseLib/tFB.cpp

commit 80b5c7c20e64cb4f937e9f7d841efe32a2ccc5e5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:09:55 2015 -0700

    cxx11 setting.

Tests/C_BaseLib/GNUmakefile

commit 6c8ab1d6f3765c60361f74c7c66f9711acbfcc94
Author: vince <vebeckner@lbl.gov>
Date:   Wed Sep 30 15:08:17 2015 -0700

    more tests for the profiler.

Tests/C_BaseLib/tProfiler.cpp

commit 89de500025f2ee39d8cb0cf6f2885a2f5b9abf8c
Author: vince <vebeckner@lbl.gov>
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 7e5a62f9f253d8943c219a9ac23e67b67cfc8b1f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7a447683d24137aeca9c759d233d7ac1bd2abdea
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Sep 27 09:58:53 2015 -0400

    some more cleaning

Tools/RegressionTesting/testnew.py

commit 3dcd5a28035c70b64c04b649c06b3278d6f57089
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a4c261757a60cf85750bf7389f79818429a31c37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 26d92a2afb7e7e360631490689e19ab57d90c827
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 15:34:27 2015 -0400

    a little more reorg

Tools/RegressionTesting/testnew.py

commit 519c16188b622cc35b4dee42e76879297ef0bcb0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 12:31:31 2015 -0700

    F_MG: fixed name conflicts

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 76f504ef7a5d21e04368ca4651844738027bd970
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5ab90cdee345703008794c88c1a7dd0ad993a5a0
Merge: 635796c ea5129b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 25 10:55:04 2015 -0700

    Merge branch 'development' into pgas
    
    Conflicts:
    	Src/C_BaseLib/FabArray.cpp

commit ea5129b473ef005eef28ed4e260f604c45d34754
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 12:41:43 2015 -0400

    remove systemCall entirely in favor of run()

Tools/RegressionTesting/testnew.py

commit d61a9f7de2c14c9f803e859de50fdfb975b05462
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 25 10:47:45 2015 -0400

    default the normal direction to 1

Tools/Postprocessing/F_Src/fsnapshot3d.f90

commit fe1d1d9468ead3291119892f4dad11a004a32219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 202bfeefcbd32be395d7334db57ae2e5cdcf83ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7057ad6cbcc325d6fc26111ba06bda26ad5a9e60
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 24 17:58:53 2015 -0700

    More typos in CMakeLists.txt

Src/C_BaseLib/CMakeLists.txt

commit d29646e510263e407ef3bb9add9508f054bde21c
Merge: 4006283 35167eb
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 24 17:01:31 2015 -0700

    Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development

commit 40062836e9b4136a330ddeb72cfba78000f10a66
Author: Marc Day <MSDay@lbl.gov>
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 35167eb1c079a24e99cbcdc8b5a8f7c061b07dfe
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c5d886735e5eb967fa3c4e785cd524199d1fe7fe
Merge: 850bd71 d458491
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 24 16:57:29 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 850bd7122e13305b20072b4158d653fede029114
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d458491af4ceecb864180c868da591b3addce04d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 10ae5250b693a25c421c4c7994c33c75915cbac4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 60a93b29b557e83a831b9f1066785d993634c1b2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 21:25:31 2015 -0400

    fix the web output directory

Tools/RegressionTesting/testnew.py

commit 4bbca85d7062a6183c4660c29aaacded32303a2f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 20:38:14 2015 -0400

    first cut at an easily parsable status for a run

Tools/RegressionTesting/testnew.py

commit 1727e668628702b632d72169085c3de3cc75287c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 42f20c9c0682b8c60a10f203aa542a65d528fa1d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Sep 23 10:42:28 2015 -0400

    bold heading in list of git info

Tools/RegressionTesting/testnew.py

commit 05e985f65348aad6556e9fa0b7ccb61664ca597a
Merge: 89e4094 575f636
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 20:24:51 2015 -0400

    Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development

commit 89e40944d914ba58d5acd864ea4cba0340534961
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 575f636ac4b4e701296e2ca27944f2781113c67f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 19:14:02 2015 -0400

    updated version of our test suite inputs

Tools/RegressionTesting/Maestro-tests.ini

commit 9e07cb3d2ef9cd58ca0a637c84501609038e7545
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 22 19:10:45 2015 -0400

    default to the development branch

Tools/RegressionTesting/testnew.py

commit 8b8e213abf3ec1a83649ef59a8b4c125f8f93815
Merge: 3c7d8a7 c2c99fc
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 22 15:46:15 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit c2c99fc0bc36035dfa6c60f32dc43c046f325f25
Merge: 70a3361 40aa273
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Tue Sep 22 11:41:52 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 70a33610df2e32551034c3628340942be67a98b4
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 40aa273e7d9dc2a9099001b2f606bbff68466758
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 16:32:41 2015 -0700

    OMP ml_interface

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit 923f329b5844acffd39c6b6bf7a5e6596aefd94a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bf8fcce72f0ed61b56e52873136db822cdb963c7.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 1fff3e0321d105980061261d80884fb8619158b9
Merge: bf8fcce c0fec89
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 12:08:41 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit c0fec89ea01c117cc814de628c6ffc7ce52d733a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 21 14:27:41 2015 -0400

    simplify convert_type

Tools/RegressionTesting/testnew.py

commit bf8fcce72f0ed61b56e52873136db822cdb963c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 21 11:27:29 2015 -0700

    save a multifab build and copy

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 428ecae8bff186c4cf91e06f53dbcd868084e026
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eae53d801410ba52ed3a62acb027b8ecc6527739
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 21 09:41:01 2015 -0400

    fix the OMP stuff in the run()

Tools/RegressionTesting/testnew.py

commit f5ae7ba29e2edc632e7cd6af5d4a1ff2378e7477
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2fc6044e460a9e4bab85f2c6075a89c10c0a0711
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 80b66ba3b009d4607b4837254a193f6ad4564016
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6c1226144412c0825d5d588881cf7b409d0965e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Sep 19 23:02:07 2015 -0400

    store the diff command

Tools/RegressionTesting/testnew.py

commit 42745e3337516991502b2a83d36703e06ec806d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Sep 19 22:32:43 2015 -0400

    switch the diff over to run()

Tools/RegressionTesting/testnew.py

commit 83466c8d48f1b5fc43f41177a69a3fdeab0e1f34
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d594b43abc040203b52a4726a696249cee705eff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c7d8a7f87431fee557b0e57acef8f7475e24d1e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 15:11:24 2015 -0700

    added profiling.

Tests/C_BaseLib/tFB.cpp

commit da884a3dcca46362c58e826549ae0138d78c989a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 17 15:06:39 2015 -0700

    added assertion

Src/C_BaseLib/PArray.H

commit b28d8375eab17dc5e4311251ad56fc89c8404fc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cc29abc83582eaf1355747248125c5a27587fa1d
Merge: 3c890f3 cca9422
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 11:35:47 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 3c890f33637d576bd01c2797be013a66b5a5cb22
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 17 11:31:14 2015 -0700

    unique set.

Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit cca9422197a9ebb28eb3056e169d684e429a6aea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 16 17:31:38 2015 -0700

    fixed a typo

Src/C_BaseLib/IntVect.cpp

commit bf1777b4fec8f931ee176ab5e5986ac95dd341e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6ace9a195b172595ac0a7275eefd5eb30f2758dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9029f08edf3818f537d0c882a96cdc7c8bc726b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7e05805531eb30c7ae25e6f193e5e1e85c558fca
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 59ab06a0f774b0e5b01bb52b17776b3f461295ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1b02ba0ea9f3b6ea3d5242765b069c58a12e263a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d78fb47e50b2b76df9cf204b3a6ea4fe8640ad0b
Merge: 41d173a 5e3be44
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Mon Sep 14 15:38:45 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 41d173a6c9919def40e6dae1073b3f3b5a88f10d
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 5e3be44245db7d4194a0661adcc64faee059ab2a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 14 11:10:31 2015 -0700

    fixed a new bug in tag_boxes

Src/F_BaseLib/tag_boxes.f90

commit c156c849c5a121d8fadda539e69d0d7756865775
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Sep 14 12:10:46 2015 -0400

    need to define last_run earlier

Tools/RegressionTesting/testnew.py

commit 21ef91afe99f4ab7cbc7dead0f7db65ef52f58cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df0c0fd8cfb3c87cde16187b48745dd2456ca016
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 12 11:25:03 2015 -0700

    tweak flags for .F90 files

Tools/C_mk/Make.rules

commit a1ef045490b30fab7d64bf74b0e5425ee06ce86e
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 0ad8689a58997ee0ab902d217a83c6fe247f63fb
Merge: 485626b fdb0b07
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Fri Sep 11 23:53:13 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 485626b2cd47786c56f7bd77f37ef44d77324324
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 fdb0b07c70365340062958d0d4c0c5af503ce83a
Author: Brian Friesen <bfriesen@lbl.gov>
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 317f40b898a76166a04dc49c1759e173204cd3db
Author: Brian Friesen <bfriesen@lbl.gov>
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 22dca70a7ea4283a597241d1fb80ccc41a0a3f94
Author: Brian Friesen <bfriesen@lbl.gov>
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 3f33379d932a12d8daab8139428fdc1773af6cbf
Author: Brian Friesen <bfriesen@lbl.gov>
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 c073c3220de39e3f49df8151044afb524d284538
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 11 10:33:10 2015 -0700

    tiling in tag_boxes

Src/F_BaseLib/tag_boxes.f90

commit 13448ab43b758fcffec5a870babba239524df837
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 11 10:24:04 2015 -0700

    added omp paralle do

Src/F_BaseLib/multifab_physbc_edgevel.f90

commit 0796be23ca2c3cbd9ada57de04ff1fd3213bef00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 11 10:06:45 2015 -0400

    fix a bug in calling list for reportSingleTest

Tools/RegressionTesting/testnew.py

commit 82b2ed2d81660b1e01ae9e4a077f078bc63cb97d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 85cbce76228e7f68a45d5cf6271aaecdf019997f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3686028edeb71299dcd6fbde3cf516e1b1f994b1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 16:21:32 2015 -0400

    fix a few bugs

Tools/RegressionTesting/testnew.py

commit a5bf611f48be45d0992151331028e39588eedd68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 15:58:34 2015 -0400

    a little more cleaning

Tools/RegressionTesting/testnew.py

commit 913fe593d74e3b61636eebf3c41bbf595cf0ee09
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f642017c59593c30d7d14aa3dcbc76cea255bba9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 11:59:34 2015 -0400

    let the HTMLTable take a list of div elements

Tools/RegressionTesting/testnew.py

commit ae36ba9b4a6a1c28a440261e408a8a12ac812b7e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 11:03:31 2015 -0400

    fix missing ]

Tools/RegressionTesting/testnew.py

commit e820bb91a994903b18fd27a3cce9fd0cb0c05d01
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 10 10:20:43 2015 -0400

    fix the handling of NaNs present in the compare table

Tools/RegressionTesting/testnew.py

commit bab2d57332da8dbe7d728ca44f44b4148e0aff47
Merge: e657004 e4b5490
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 9 21:03:30 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit e657004b80b8b85b35d390b9f496f2929e7b0da4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e4b5490188233f38d34dff069194037d6e0e5600
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 242f1b742a40b463922bbd7cc7c977d21f1b9e56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7abac98be677ccb45bea53dc43560b84ffb12cb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 635796c462765b19e0e70dd7e22e041bcc8b67a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 277a773c13f9c61543384f5d36e2023a9652e39d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 8 13:12:03 2015 -0400

    some css tweaks

Tools/RegressionTesting/testnew.py

commit 694b18635a5c2c2eab915084f38ee260a26e9f8e
Merge: f981ba3 3df0177
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 8 09:58:47 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
    	Tools/C_mk/Make.defs

commit 3df0177ce2f059f3da1226bf4fb8c206efb05ffd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 d8bb1ec526b388a7a949ff667c0e33fd093f3132
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 8 09:42:32 2015 -0400

    fix ordering of hash and branch in output

Tools/RegressionTesting/testnew.py

commit 371058511816234a6e7531acff2efc7bcc757ed6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5bc3e2e9253a0ede2b063c9ec8e003fc4c92e9f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 14:46:51 2015 -0700

    more tiling

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/ml_cc_restriction.f90

commit e8e8a4226bc2a8f29deba537b24d70751881e78d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 79484cc2b8b8fd519253d971adbc88e4ae05d278
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Sep 5 14:23:07 2015 -0700

    always include sstream

Src/C_BaseLib/BLBackTrace.H

commit 92b478bd53475d666742aee71d6714834fc5fdb5
Author: Ann Almgren <asalmgren@lbl.gov>
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 21f4fc7a0c083df75208efa3ea3aae1d463b9dfe
Author: Ann Almgren <asalmgren@lbl.gov>
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 07e7083491dd89c38ec8de7e930117c043471570
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 08a44f63460c56ed6257dfdbe92aa24c33b8e8c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8a6052e4cc8aa42ad2b83feb3bffb26ca682b76b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 4 11:57:56 2015 -0700

    minor changes that can cause roundoff errors

Src/F_BaseLib/multifab_f.f90

commit 637f78d7b0410eafee8b5b7de7a021996c80aaa9
Author: yzheng <yzheng@lbl.gov>
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 6986349a9623f6bd12dedf166473fbe6666abc5b
Merge: 1d3dc73 f981ba3
Author: yzheng <yzheng@lbl.gov>
Date:   Fri Sep 4 11:05:09 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 8ad70b4e6a3578618895b6750bf2aace6f311bcc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 11:03:41 2015 -0400

    fix a link + pretty up some CSS

Tools/RegressionTesting/testnew.py

commit 4dc415c1a2e35f3135a8e775dc59c8e01dba6c38
Merge: afda0e5 7bd027b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 10:01:36 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit afda0e5a6a8d22419c2fe9cb6f5784b5ad5f7447
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 10:01:16 2015 -0400

    switch the test run overview talbe to HTMLTable

Tools/RegressionTesting/testnew.py

commit 7bd027bac11ff47dc3bd8b1ba9ac6ce59e176d53
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 09:28:36 2015 -0400

    wrong indentation in the MPI call

Tools/RegressionTesting/testnew.py

commit 63b472b1803dba0c71c697a374184c1060674fc6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 4 08:27:55 2015 -0400

    catch when boxes don't match in fcompare

Tools/RegressionTesting/testnew.py

commit e6440c7db5cda8f052f72fc23019d36ddbff47f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 20:53:44 2015 -0700

    tiling

Src/C_BaseLib/MultiFabUtil.cpp

commit b3b6a47f8863e94f7f64e8ab71ef739ba1894bad
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Thu Sep 3 23:38:33 2015 -0400

    Fix minor bug in assertion

Src/C_BaseLib/MultiFabUtil.cpp

commit 70423254b1688c33412658baac2720f3dac3be8f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 3 21:17:33 2015 -0400

    a bit more restructuring -- moving things into the suite class

Tools/RegressionTesting/testnew.py

commit 2a62e48f4040e1b8117288a9cdd6c5ac39d3ca9c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f603d5f1030e18ef2fb0b773a46da2382082cd7f
Merge: 26d913e 5112ec9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 3 14:47:27 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 5112ec905771fb43e9b0fc34fd1393bc69618ade
Author: Brian Friesen <bfriesen@lbl.gov>
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 26d913e828d25fe4257a32299a71fd30bd942866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f7f5de123273f49e7a6f672ecbd6d57baa559734
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e0717fddd3a7f54d710c705903f3c7f3741d8874
Merge: ea3c610 266e1ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Sep 3 09:57:35 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit f981ba3516b11421a113fe9133f143fcf3ccbe55
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 2 20:40:23 2015 -0400

    added bl_profiler

MiniApps/PGAS_SMC/main.cpp

commit 266e1aee0f4b1887f3f59450f4d802f5b6029735
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 2 10:44:38 2015 -0700

    minor bug: used optional argument without checking

Src/F_BaseLib/make_new_grids.f90

commit 22f812cf5ef0888215f717f85d2fdae31aa400d5
Merge: 83aa2b8 5abc60a
Author: Brian Friesen <bfriesen@lbl.gov>
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 5abc60ab022092045410177fa0ee50a91357ed70
Author: Brian Friesen <bfriesen@lbl.gov>
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 b2bc2eeee282c88c36c1a1300ab7c0d7d54ba914
Author: Brian Friesen <bfriesen@lbl.gov>
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 0e12d1dda300ed37a9f10996f7f848312b42ea14
Author: Brian Friesen <bfriesen@lbl.gov>
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 83aa2b82a074305df72d5a1f6a3aec5616b40a80
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:46:04 2015 -0700

    fixed intel compiler macro in last commit

Src/C_BaseLib/BLBackTrace.H

commit 99907183e4686a9e5a30e70bca56c63c6db9f015
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1ce3f9801b756c1dc6e66edc0be19ffba3d33984
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cb86fba6ab3d8dc1e8e816c519a7c350ba6231ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 17:24:38 2015 -0700

    added -g to Cray

Tools/C_mk/Make.Linux

commit ea3c6107ff3d5e421f0d4f10f865f79ae2c3087f
Merge: fcd46eb 7a8a530
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 19:35:39 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit fcd46eb777054faf5c4e578a32a9cdc2be0a86c3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c7dbfb89ed7fb96759aa6848fcd493d333e5eaae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 14:19:46 2015 -0700

    make Intel compiler happy

MiniApps/PGAS_SMC/SMC_advance.cpp

commit 7a8a530882089b7dd08169467c9ad88afcc49ab4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5bb2e4d0c3baf827e73c37dc410682b05c26578f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3bf18a9c52e21519951602b7738ff8e3fc30a8c6
Merge: 15a52d0 6930a6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 12:05:09 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 6930a6b35ce8998abf58fe00ee100464e9796cdd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 15a52d0892307c44861868473b88c3dd28bfae2f
Merge: b1ca0c2 9c962d1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 11:50:05 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit b1ca0c239f064cbfa7212b0c0345d04ce24f3065
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Sep 1 11:49:56 2015 -0400

    add an equal method

Src/F_BaseLib/multifab_f.f90

commit 9c962d1c2a8fd7edb11e2be614649ec168fdcde2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 1 08:30:27 2015 -0700

    fixed a new bug: forgot to build mfiter

Src/F_BaseLib/multifab_f.f90

commit 4c8a14ea9fb271a958a36af99e4bff0b61bad48a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 31 17:44:20 2015 -0700

    more tiling in multifab_f

Src/F_BaseLib/multifab_f.f90

commit d23f672c4b4c4568b03b44f75497b55a820bbd6b
Merge: 90a598b b1e9fe5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 31 17:19:02 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 90a598b3cdb62ea2978980e8486596d9ca8f3dc2
Author: vince <vebeckner@lbl.gov>
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 439ba4044c9e689845aaec3b6adecef75425cdd5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1e9fe52d747b582c18de532c9dae23034dd05ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 23:41:43 2015 -0700

    fixed a new omp bug and cleanup

Src/F_BaseLib/multifab_f.f90

commit dd986a0a2036c3faa19f131f2f7667b584dae8ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 22:30:54 2015 -0700

    fixed typo

Src/F_BaseLib/multifab_f.f90

commit 34bc454266101d285615adfd1162486db2b61590
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 22:15:21 2015 -0700

    more tiling and forgot to build mfiter

Src/F_BaseLib/multifab_f.f90

commit ed06581dd8178f62e0498b4a8ed5e1db6509b947
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 791a95df95a034f11d07a2656b1345ceece37282
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 29 21:46:48 2015 -0700

    tiling in multifab_min

Src/F_BaseLib/multifab_f.f90

commit 6e9de507b0ac244671cb9e1f747c3d4bf9e7a24e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d2254b328ac25b69ffdaf70ce7d532a508af4583
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ce00022119eb1037a51a216a9d9515702ab74893
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 17:01:48 2015 -0700

    more tiling

Src/F_BaseLib/multifab_f.f90

commit 3c83464587fc07a439bdbd47bc93b6eb562fabcb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5f0c809782930a5bd04bb8145f334d8928c0f602
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 16:52:02 2015 -0700

    handle empty box in mfiter

Src/F_BaseLib/layout.f90

commit 3550f7a84153dffbecaf3a3044508293d23008a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 28 16:18:13 2015 -0700

    tiling and omp in multifab_f

Src/F_BaseLib/multifab_f.f90

commit 2cc6fdf3524b121922c4a7f86eaefc8117f22326
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1d3dc73c93ee71fd205debc73e0d52c13dc5528d
Merge: 156cd26 6cdabe5
Author: yzheng <yzheng@lbl.gov>
Date:   Sat Aug 29 15:55:46 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 4fc73359556090eedabdb23c92ebd4d68b81e1b5
Merge: 1af02ec d89db3e
Author: Max Katz <maximilian.katz@stonybrook.edu>
Date:   Sat Aug 29 01:51:10 2015 -0400

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 1af02ecf86d4ade6bf75416cb188d5cdcbc9c30a
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 d89db3e6dc492a86956ab5bd13342c063984857e
Author: Brian Friesen <bfriesen@lbl.gov>
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 63036a25a575ff29e7cbf0e7714b88b003a7e359
Author: Brian Friesen <bfriesen@lbl.gov>
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 6cdabe5c98c8d26b3355f102a753ba48ab6e147e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d3b7e7e3a390367e320f9e5b8d61178bc3127dc0
Author: Brian Friesen <bfriesen@lbl.gov>
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 8ed2642b6f37cb137bb4c386be68748a46118bae
Author: Brian Friesen <bfriesen@lbl.gov>
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 763ba4d49b6394d29ec511527f687464006bc71d
Author: Brian Friesen <bfriesen@lbl.gov>
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 fddeab5f255c416541df215dbaa142e6d1f707d3
Author: Brian Friesen <bfriesen@lbl.gov>
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 45789ea132a1576f536dae4d614d58daa6e4d4ec
Author: Brian Friesen <bfriesen@lbl.gov>
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 e90ccdf0b5ff6e72110767c364ff91368e4249d6
Author: Brian Friesen <bfriesen@lbl.gov>
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 8c89549a4222d91cee02ae84330c8a761a7492fe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 17:13:41 2015 -0700

    split FillBoundary_finish into two versions: MPI and UPCXX

Src/C_BaseLib/FabArray.H

commit 156cd26bd6bbb292f9c9c39b15d4183b35ed2483
Merge: 84e9b95 397e83f
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Aug 27 16:42:55 2015 -0700

    Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas

commit 84e9b950f7935d2eab4d482ef6e1bc12c4e9f131
Author: yzheng <yzheng@lbl.gov>
Date:   Thu Aug 27 16:42:52 2015 -0700

    Use UPC++ barrier for the UPC++ version

MiniApps/PGAS_SMC/SMC.cpp

commit 80140ecde6e9913fe4ede35b21d2021eae313589
Merge: 397e83f 801b617
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 16:24:34 2015 -0700

    Merge branch 'master' into pgas

commit 397e83ff7937c1ebc33cd559676095af0ef69233
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 27 15:22:44 2015 -0700

    tweak the output of timing results

MiniApps/PGAS_SMC/SMC.cpp

commit 801b617be12365d62f88c954a3096d3559ea8870
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Thu Aug 27 14:37:23 2015 -0700

    Geometry: add forgotten assignment of is_periodic in SendGeometryToSidecars()

Src/C_BaseLib/Geometry.cpp

commit d4dd720b7030345420f4070feed510f4a2ae11c9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4355098d0971a5b414bef1f5526bede587f4f533
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 62b6f3599e5554d1ced4280e2d72e5d1b88681de
Author: yzheng <yzheng@lbl.gov>
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 e34ec68165726165e1b85f3079442416d32da888
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 4ac481778ecc899c17c5ea36a194143c80d6d4f2
Merge: 6b8b681 4e06e6b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Aug 27 09:16:15 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit 6b8b68172b789d81f15b97eff96e46a8ab93ff65
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a479b3ba6ecc57016666e412ce64d6bb976440a9
Merge: b5d1d12 4e06e6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 15:05:06 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
    	Src/C_BaseLib/BoxLib.cpp

commit 4e06e6b1b63056b2054d3ed367f5ba0a4f5aae5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b5d1d12de5b1b003522bca018d98ffa8aef74520
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8f1bd4a384508ad2664b0abbac4041ac57a3fe1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9170ed1176b3e750cbd25060e434c5f2cc861b1a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 11:01:53 2015 -0700

    PGAS_SMC: changed the default max_grid_size

MiniApps/PGAS_SMC/SMC.cpp

commit 9b79e409cc680189cf826bdf96e7e6d3c688d9a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 26 10:25:50 2015 -0700

    tidy

MiniApps/PGAS_SMC/SMC.cpp

commit cc5d3c0bda4cbfeff2887658228a8a2e52665221
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bae28d55a3d36c647b5c1533accaa3af54885f24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 28f46dcd6e53e5a672e233bb503ee2da47d60549
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 64064be9bea4012af0f0b6376406d7b2ab61ee2b
Author: Brian Friesen <bfriesen@lbl.gov>
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 94665db28cd82f2646de87b357396fb5afd6b114
Author: Brian Friesen <bfriesen@lbl.gov>
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 7ee82d882edc872cb22d2bd7a126c6e7e19ce3ba
Author: Brian Friesen <bfriesen@lbl.gov>
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 b26fa9eb0eea002ab097d21d1fc7871245ad6dfb
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 25 14:26:56 2015 -0700

    ParallelDescriptor: compactify pointer allocation syntax in SidecarProcess()

Src/C_BaseLib/ParallelDescriptor.cpp

commit 8b9e73dcb7a3dbe40bbb76c15fca60c35f8df654
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 25 13:19:09 2015 -0700

    fixed typos

Src/C_BaseLib/BLPgas.H
Src/C_BaseLib/BLPgas.cpp

commit 1f1b768d763223b7e82a4ca7174c74a48ac05f2a
Author: Brian Friesen <bfriesen@lbl.gov>
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 205aadad75b58a649d6cefe628ee793534e303c2
Author: Amir Kamil <akamil@lbl.gov>
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 93ed9e20b57268608cd2f4f503bed1a64eb4db3d
Merge: 3af81f6 0239566
Author: Brian Friesen <bfriesen@lbl.gov>
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 02395661308319fa097d8f556dd351dca1915809
Author: Brian Friesen <bfriesen@lbl.gov>
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 7dfda73ce337ceff2f8a4a4a9f91ab66707f559e
Author: Brian Friesen <bfriesen@lbl.gov>
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 8022d0c677a69c333b567a99caecbd0c9cfdec8e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 24 17:23:27 2015 -0700

    flesh out 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/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 3af81f60658bc0f173db56e2128f2e2ca30f9556
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dfdfe3386dd788c108f58e2ef5908a413324fbbf
Author: yzheng <yzheng@lbl.gov>
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 78ee54183babdee46c65d5b78e22eb34f6db3f6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 21 17:08:25 2015 -0700

    fixed wrong index

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit abc69ea34509d0e8be68ee67b7b595fea6a877c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9d75234a02079e1d84a6f18ef4a8da20ca851520
Merge: 61d522c 8c18d1e
Author: Brian Friesen <bfriesen@lbl.gov>
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 8c18d1e3ebaa0353a3ade738fe3fbfc273da0e4a
Author: Brian Friesen <bfriesen@lbl.gov>
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 f7fbe8d95a5c5f7479862a7455d2b0b786bb554a
Author: Brian Friesen <bfriesen@lbl.gov>
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 493a2674a25400a55eadc508a75a0fba9a423e6a
Author: Brian Friesen <bfriesen@lbl.gov>
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 d83fac4eabdfd604100e514ee9fbaf5ef6fb4d2b
Author: Brian Friesen <bfriesen@lbl.gov>
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 e8ed87d3ae88114fbd21cb445ae4b2248333ae00
Author: Brian Friesen <bfriesen@lbl.gov>
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 83d7fd630b6209d33a90b380d066149190f79cf4
Author: Brian Friesen <bfriesen@lbl.gov>
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 79db42d4246379b7c8a3d1d7d3272b704d4ee0f7
Author: Brian Friesen <bfriesen@lbl.gov>
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 1b2de8eaaddc8f7708f0382f77cc80c38da1d7fe
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Aug 11 11:15:03 2015 -0700

    DistributionMapping: added define() to build a DM out of an Array<int>
    
    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 64dd430c74d412ac6cb0fca3db87df852b4a8e44
Author: Brian Friesen <bfriesen@lbl.gov>
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 7d8119a3679b9827704e16ffda9a6dbf56a27415
Merge: d662076 61d522c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 61d522c84be722477d4bd47c5f611a031d76f22c
Merge: 835c29d 99d6969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 19 17:45:47 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 835c29d7162c54e7081525d8dedcede22cd7ace2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 99d6969dd18fea3a9255eda83cf1f67740fcb99d
Merge: 41da531 395fff2
Author: Brian Friesen <bfriesen@lbl.gov>
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 395fff20b2c4f4f2fedae044c075e2de07eff92c
Author: Brian Friesen <bfriesen@lbl.gov>
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 6e86d97059cf64947ba3a10d2c8152640568a259
Author: Brian Friesen <bfriesen@lbl.gov>
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 41da5318c0b1111c7f7afa15cc52ad998c6d4910
Author: Brian Friesen <bfriesen@lbl.gov>
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 d662076d2c222950d29af719fb425e6f7fe19197
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 33b96aa4b5bb94a2c63479436c23df2eb7783e86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Aug 18 09:55:56 2015 -0400

    add a subtitle to the main test page

Tools/RegressionTesting/testnew.py

commit 50b6a24b64adfbec80ecea3c9ff9f2ccba70f107
Author: Yili Zheng <yzheng@lbl.gov>
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 5a96e4d68283bcb023789d84a5c4251ce6432207
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 14ee982afd07f5f12829dd394ba6de7846691c9b
Merge: d433587 6dbbd3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 15:04:58 2015 -0400

    Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib

commit d433587597891c02c2689917f372f086a0387d24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6dbbd3caa6fe704f6a1e535a8814408423381b86
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 13:48:11 2015 -0400

    make the tol 1.e-6 for highlighting

Tools/RegressionTesting/testnew.py

commit 15c393241ae627c000b092f7ba0ab583a97c1c20
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 13:31:39 2015 -0400

    new test comparison table with highlighting

Tools/RegressionTesting/testnew.py

commit 8998acd991e62278848bc4732324ab7ca9ca24d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Aug 17 10:53:31 2015 -0400

    close an HTML header

Tools/RegressionTesting/testnew.py

commit d2873ed7e1ef4561c9d770e528e4e792eec4a7bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Aug 15 18:56:04 2015 -0400

    update comment

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 98367418c18b63fce13f3767e5eb79d3f617abd0
Author: Ann Almgren <asalmgren@lbl.gov>
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 442ec75650ef3db60673958c098f19e46e76c9e3
Author: Ann Almgren <asalmgren@lbl.gov>
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 3deb0a736272a528e9de4d71628683b18a06715e
Merge: 563fd47 8a8ff83
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 14 10:29:43 2015 -0700

    Merge branch 'master' of github.com:BoxLib-Codes/BoxLib

commit 563fd470749f7861fd62653fd784f1644edc96e9
Author: Ann Almgren <asalmgren@lbl.gov>
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 8a8ff836d2297951972dd03196933ca43c54a8ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 13 11:32:21 2015 -0700

    fixed periodic boundary and a local index bug

Src/F_BaseLib/bndry_reg.f90

commit 0155e668db5814f3924502b88de6f101d3f87bd9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 13 06:45:39 2015 -0700

    delete removed variable 'id' from omp private

Src/F_BaseLib/bndry_reg.f90

commit 731fff37e42deb6eb504bcd2ebb1696c9720c550
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7626e166aabc8eecb5eb4f8b1685774f3733707e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 12 11:11:27 2015 -0700

    print more information

Src/LinearSolvers/F_MG/ml_cc.f90

commit 3ae839d7ffdf826dc2c14f664d0871246b169eaf
Author: Max Katz <maximilian.katz@stonybrook.edu>
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 1fac90ac4aef4f0f2467081a1ba62f04dd71d91e
Author: Ann Almgren <asalmgren@lbl.gov>
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 2123b517be444d4937ad08f5dd69361bcf9f8daf
Author: Ann Almgren <asalmgren@lbl.gov>
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 75a6c59bcbb5a38461b892c1fa51a03c5152cf08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 11 11:37:55 2015 -0700

    use std::pair<int, FAB *> instead of std::make_pair<int, FAB *> because the latter does not work in C++11 due to template type deduction rules

Src/C_BaseLib/FabArray.H

commit 5e64772cee41eb4aea4753543c843a5b30954f5e
Merge: e8954cf 1b44cbe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 17:43:43 2015 -0700

    Merge branch 'weiqun'

commit e8954cf81f29f07ea72fa4a382a38e8cd6df1b9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e161371d033a4ed3b3a4f6fee2e3f578ff68bc3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f2958a6aaf9438af0b17643ef0a914fb99d9498b
Merge: 2b4db8e 009503a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 10 12:58:10 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 2b4db8e318c26d24e62badaed16ac27dcdbeecee
Author: vince <vebeckner@lbl.gov>
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 009503a63db2da581665a3aa34e2a407c08626cc
Author: Brian Friesen <bfriesen@lbl.gov>
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 1406a2c601cb3258103d1f1cbfc2608eddc584c0
Author: Brian Friesen <bfriesen@lbl.gov>
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 074781ba770bca63d6f037b092eeb3df7a14c339
Merge: f334cac 2df9230
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 10 11:03:06 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 1b44cbefd2ad2ddc8edeb851a7e3f400fbe09e07
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 10 10:59:04 2015 -0700

    Avoided allocating temporary multifab in multifab parallel copy

Src/F_BaseLib/multifab_f.f90

commit 68785531edeaa79f779a68801f1b6387ed7d7eb3
Author: Yili Zheng <yzheng@lbl.gov>
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 0a5d0b6586e3c18b998fd1d6fa56974c3abd032a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 6 14:57:48 2015 -0700

    fixed typo

Src/C_BaseLib/Geometry.H

commit 77b2b36dfdbcdd9994790e7636948e5233cee632
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 835fc68e681e462cc84e07f049f83e9b0bd96aeb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e92de81e66f6f375f98b1aa228fa6847c1c9caa8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d8ade2087159112d8ccf988bebabebb5d86ab2f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 12:22:33 2015 -0700

    fixed merge

Src/C_BaseLib/BoxLib.cpp

commit f260a60c58188ef613980366d89f9943b3d06ac9
Merge: 3e5d35e 2df9230
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 10:37:11 2015 -0700

    Merge branch 'master' into pgas

commit 2df9230407f01dcdd087161811600efc518b14e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 5 06:42:16 2015 -0700

    fixed undefined reference to 'boxarray_build'.

Src/F_BaseLib/fabio.f90

commit adbaa83cf6fa6afe4b19562e3594c3483c81f234
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e74057fda0a81e54e0c8f62c9cf29a97ae2d73e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 17:16:55 2015 -0700

    simplify parallel copy in bndry_reg

Src/F_BaseLib/bndry_reg.f90

commit 083710175605663fa110ba6a33db46fea86b3f09
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 17:02:03 2015 -0700

    added omp parallel do in bndry_reg

Src/F_BaseLib/bndry_reg.f90

commit ed17e531a3ad2e32bab68b50a8488a0b1cc38db8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 4 15:52:56 2015 -0700

    use bl_allocate in vector_i module

Src/F_BaseLib/vector_i.f90

commit 6d13b9018ee500169967fffd9bedf50204f0e25c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 598cdc75c6e229e66b9118e75b5c27588aa3560a
Author: Marc Day <MSDay@lbl.gov>
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 f334cac5f9f94e47734da3e844184d7b5ae90bc0
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 4 12:15:36 2015 -0700

    itac suffix.

Tools/C_mk/Make.defs

commit bc361948e69f9648361397d4ce7c546ea19a12cf
Merge: 63d055a f8083db
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 4 12:14:07 2015 -0700

    Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib

commit 3e5d35e86f45b4c03adedc76adc6fdcf260fc032
Merge: b03d062 f8083db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 3 18:18:56 2015 -0700

    Merge branch 'master' into pgas
    
    Conflicts:
    	Src/C_BaseLib/BoxLib.cpp

commit f8083db8208690d812e53247da897cf96a40e380
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b03d062a11c392d8d170425094af50b1ad2c56b3
Author: Yili Zheng <yzheng@lbl.gov>
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 9d8c4f5e9796900cabf5089eb239649048e0f160
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 3 11:18:34 2015 -0700

    update url in users's guide and test mailing list

Docs/Introduction/Introduction.tex

commit ca434d19d355ab92e56b06a75666bb26f13a5bcb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 31 15:21:10 2015 -0700

    made 1d gsrb truly rb

Src/LinearSolvers/F_MG/cc_smoothers.f90

commit 526b09deadade958394423ab8540266fe02eac68
Merge: 6a21226 4afa62f
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 31 12:26:02 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6a21226369971af9b1b3762be1800c73d4e8bcc3
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jul 31 12:24:57 2015 -0700

    Update release tag ID

Tools/CMake/BoxLib_Version.cmake

commit 4afa62fd8a688e79913e6ef37b48f3d6d1ec5727
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 71924a551612ff495bd9451d70268e9e9ea363a4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6a80103f32394517d5e767cf5783b58a9fc62a1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5fd7d2afe2522c53a52986c1a32a0b9df7239282
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jul 31 10:50:30 2015 -0400

    fix the --complete_report_from_crash functionality

Tools/RegressionTesting/testnew.py

commit 1c11606f6ae4f792415b7c75103537f78b96c079
Author: Marc Day <MSDay@lbl.gov>
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 f1313d19a53e7cb4ba83d2c6ce051cdb7b988d1a
Author: Marc Day <MSDay@lbl.gov>
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 7ee4ffe2b2814056a324cefea363298f96151774
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 29 14:31:54 2015 -0700

    touch the memory pool in mempool_init()

Src/C_BaseLib/MemPool.cpp

commit 6a111fa2a39aa5f791ad801b6545b5fff4ec7fdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f8d6dfcbd9616749bfa1ba409846ca545633b75c
Author: Brian Friesen <bfriesen@lbl.gov>
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 3240f8c8821d64b61e087b0c7586044a8c8bb56c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 16:57:09 2015 -0700

    fixed 2D tilearray_build

Src/F_BaseLib/layout.f90

commit 87666d0beb7d9217b3de62bb26699969018a12dc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 16:29:35 2015 -0700

    PGI: link to cpplib

Tools/F_mk/comps/Linux_pgi.mak

commit d0ccce487c27a1d3f3e9bdb8c4663467feeec798
Merge: 48297cb e552e30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:32:31 2015 -0700

    Merge branch 'mempool' of gamera.lbl.gov:/usr/local/gitroot/BoxLib into mempool

commit 48297cb17ba681471e208dcdcba4c4c8fbed13dc
Merge: c1e42db cb95de3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:32:07 2015 -0700

    Merge branch 'master' into mempool
    
    Conflicts:
    	Src/F_BaseLib/multifab_f.f90

commit e552e303f78a23cba494e50fa8d35b060bd5a5dc
Merge: f62a2b6 c1e42db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 28 15:29:57 2015 -0700

    Merge branch 'mempool' of gamera:/usr/local/gitroot/BoxLib into mempool

commit c1e42db7eed9994a0ef8a7f2a4025c641b1df0a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b9b8a0bd53a5cedf3f7720138b4f52f446f688ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 28c9945a0ddc4a1c830eb2d46a0ec2dffd600cc0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f62a2b699c043bf3922ab1bb809898d1f8a932a4
Merge: 5809209 cb95de3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 27 17:06:58 2015 -0700

    Merge branch 'master' into mempool
    
    Conflicts:
    	Src/F_BaseLib/multifab_f.f90

commit 5809209638035fcc653c5a623b941ce8ce01872e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cb95de3d06d1e5a60847b88545832c7b2ee51402
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a888edd3bd030cee2e0d2340ef76eab14a0df3ee
Merge: fb9ffe6 6927ff2
Author: Brian Friesen <bfriesen@lbl.gov>
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 6927ff2b04f2b9d5d667b0dbf393d842cc7caf61
Author: Brian Friesen <bfriesen@lbl.gov>
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 f0ea1627d915c44e63af55b5291422389a288fef
Author: Brian Friesen <bfriesen@lbl.gov>
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 2c822ab81ac5519e1d27612f9d6e8c31d6222010
Author: Brian Friesen <bfriesen@lbl.gov>
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 92e684cc9567e7f21327d6b7d0a5cfaf9938bde4
Author: Brian Friesen <bfriesen@lbl.gov>
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 d8719919360b518bdab7098702359ebcfc84c873
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Tue Jul 21 13:45:12 2015 -0700

    ParallelDescriptor:: remove some roll-call print statements

Src/C_BaseLib/ParallelDescriptor.cpp

commit 7b9c88477e4d27fe47c55d2c516d68b12686e246
Author: Brian Friesen <bfriesen@lbl.gov>
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 bc6eec4fdb0513d52a4d96722c9af292a73c339b
Author: Brian Friesen <bfriesen@lbl.gov>
Date:   Fri Jul 24 15:12:55 2015 -0700

    ParallelDescriptor:: rename "perfmon" -> "sidecar"

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 609a57546fa796ecb8d25e18f03b64577ff254fd
Author: Brian Friesen <bfriesen@lbl.gov>
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 fb9ffe60e2eb7523a5c60ebe8ee7573e19d26399
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 012169ecb10c72245db547e432675b4e5df34f7f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 772b8dddb8d13ea99210bdae069808b0fd7b034f
Merge: 0b0854b 102b7c4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Fri Jul 24 12:59:08 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0b0854ba38c00333a759402f907270b75243ebc5
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 0f271fba815491db8473646d8fa60eef1e56add5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 18aa5bec14072784354ea28333761f98cb29c34d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 15:04:30 2015 -0700

    added CXXFLAGS for Intel in Fortran makefile

Tools/F_mk/comps/Linux_intel.mak

commit eebd105f3ff87e84a373a6f98655eebe2ae56221
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 14:59:05 2015 -0700

    each thread must destroy its own memory

Src/F_BaseLib/layout.f90

commit 95c9ad785e599821fb8478544fcc395133f18c21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jul 22 14:06:25 2015 -0700

    new makefile for Fortran

Src/C_BaseLib/GPackage.mak

commit 1274f7c37943e4c2e7620281ecdeec5bcc7d82ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 102b7c4b0ba77ac9906a5bfdb00594484328a9cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ef3a00810888b8ebdfbee0de5276d63d38543075
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bf8814168e0e0f6134cff41b6ce3b3c84d703fa9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4215412c02685a29c2212dde9845da3398ef846a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d2e6961a9f32e592c1788b7cdb701a72ab413884
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 20:53:32 2015 -0700

    identation

Src/C_BaseLib/FabArray.cpp

commit dd65a7e3b35e3e26c8c65848c825ecb4d37022d2
Author: Marc Day <MSDay@lbl.gov>
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 cfadc04dfc88ff35425801b8319f23a92d398d7f
Merge: a6e4f79 1bcb01e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Jul 20 18:49:52 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 63d055aa7a96f1e5418a1a84158397c7d306ac43
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 16:45:19 2015 -0700

    swap pair test.

Src/C_AMRLib/Amr.cpp

commit 1bcb01e95616b1ad5b3ed5e66bd462cab5b75d94
Author: Jessica Kawana <jkawana@lbl.gov>
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 652b4bae385626b8262e467c66b567fecc09abd2
Author: Jessica Kawana <jkawana@lbl.gov>
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 54ffe9ddb577935883ef5c06693f724548fa04bb
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jul 20 13:18:05 2015 -0700

    Added timer

Tutorials/Tiling_Heat_F/advance.f90

commit 1aebdb969c75e8bc62cea116995ff168a0a5f13c
Merge: 52dc3b8 3104d53
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 12:09:59 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3104d53e63819dfe01e9152f857249d849921c47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 10:54:53 2015 -0700

    fixed uninitialized values to quiet valgrind; added some comments

Src/F_BaseLib/layout.f90

commit 9b5255b025cfdc0912b1acd03c1eaab98e2bebde
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 20 10:51:00 2015 -0700

    end if -> endif

Tools/F_mk/GMakedefs.mak

commit 86221be96f54977d73bca260d46a1ade921bd2aa
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 20 10:48:39 2015 -0700

    if compiled with MIC=t, add .mic to executable

Tools/F_mk/GMakedefs.mak

commit 52dc3b8ab7c98a15ca29eca5f481c16f9ce066cd
Merge: 8144956 acc5d3e
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 20 10:45:49 2015 -0700

    merge conflict.

commit acc5d3e0776ab757d9edbd6d8e0d67100f9e91a1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 10:26:21 2015 -0700

    fixed a new bug in FabSet: wrong source index

Src/C_BoundaryLib/FabSet.cpp

commit 5fed13edfd7db24f68635f2214d87d516bec55a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 06:56:16 2015 -0700

    fixed another new bug in parallel copy

Src/C_BaseLib/FabArray.H

commit 566745cb1815c86b369d58c1be2a111e2aa7ed96
Merge: 75b5e7a 31fbd4b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 20 06:16:52 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 75b5e7acafdf6cb19d7e8adf8fcd2e5ee8ed8cf2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 31fbd4b0e71fa9c42b48d86050762379ed6ec5f7
Author: Brian Friesen <bfriesen@lbl.gov>
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 fefd7b32e66e4024e969024a69655a63b3077f77
Author: Brian Friesen <bfriesen@lbl.gov>
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 0088baebef159bd3a53d01a0726be7026261a8a1
Author: Brian Friesen <bfriesen@lbl.gov>
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 4e298b046a919c0ae0fbb80e4b6ad9c96b9e75b5
Author: Brian Friesen <bfriesen@lbl.gov>
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 4d584f2995b548dd532d2c6419b7a23c45ee0faf
Author: Brian Friesen <bfriesen@lbl.gov>
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 cbb1c3e88c10cf16515479f883de3e139fabd26b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 742cf9625500e11ed07cae7c8a9b633220f4e7ba
Merge: 03e501a 9080603
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 19 06:55:19 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9080603c55391900bdb1f01682627a1d7b89d644
Author: Jessica Kawana <jkawana@lbl.gov>
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 6990535aa1199be0089ef7b0eb98deb786284833
Author: Jessica Kawana <jkawana@lbl.gov>
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 03e501ab5bdb6f229c15f8e07e54563bb21d0eb7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d3065390639a3727206e8bf7c830ba86a7e5b0ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 17 14:50:11 2015 -0700

    comment

Src/C_BaseLib/MultiFab.H

commit 086ebcdbec9b427217a7b6fa642a72595f71eaf8
Merge: 08de965 96d26c4
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Fri Jul 17 13:08:16 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 08de965ce4872bb0334df6918c09895c18960494
Author: Jessica Kawana <jkawana@lbl.gov>
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 97b5aab3915f038a9c773fb9fe531806d02bb36b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 96d26c4f87178fc23a2596d6d119b3786f585c34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc3ba0fc1e58eff4b9c95cc8c46b911e8b46d886
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 15:34:44 2015 -0700

    fixed a new bug

Src/C_BaseLib/FabArray.cpp

commit 84c5eeb162d9f0a7e0c7e07833cf64caf2d72486
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 df445133f74b0f2db3405ffaa8e876c1cb6c7378
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e8ffcb57a154ac3db874e634d3060c19e957cc21
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 16 14:14:20 2015 -0700

    Fortran mfiter: added get_grownnodaltilebox

Src/F_BaseLib/multifab_f.f90

commit cd661e187a9ce64bc7f68fa14c79182f388dc44d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 81449569b5c59058297aec37d810768d5b46465e
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 16 13:06:59 2015 -0700

    more random cluster tests.

Src/C_BaseLib/DistributionMapping.cpp

commit 1a3057ea8836a677fc0cd3d57146bdba4ff68fba
Author: vince <vebeckner@lbl.gov>
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 6aa65e7a3a739e5900086152b6446246f1d1bb02
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c7f210f45a177c72ff33dc2c886e8342f1d592e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1df5aacba20673451eb699e4b45587becd7f4ed0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9194883963124b6d842de1ecb0ca16fcfa3ebd74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e283ae9fdfcf1b730acd349f4badb0d33d71a212
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6e7927fa87626e4c329286695b5b4713d9e12e85
Author: Marc Day <MSDay@lbl.gov>
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 f6bfa9ab94ec752bd39b35fe9b79b889e6093216
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 14 15:03:13 2015 -0700

    staggered cluster test.

Src/C_BaseLib/DistributionMapping.cpp

commit d057f983f778cf6e27ee7766bfdca0fee85a2d7d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 14 10:20:33 2015 -0700

    initialize the timers

Tutorials/HeatEquation_EX1_F/main.f90

commit 44095aca66961d299288690e00fdcaa291e141da
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 14 09:44:29 2015 -0700

    add some timers

Tutorials/HeatEquation_EX1_F/advance.f90

commit 99c4ff052cb2f2802c6f1b14017b0bcfba907908
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 13 16:56:22 2015 -0700

    more staggered grids.

Src/C_BaseLib/DistributionMapping.cpp

commit 85116c6290ef03c0493e45948dbd361d72748466
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 13 16:52:36 2015 -0700

    more staggered grids.

Src/C_BaseLib/DistributionMapping.cpp

commit e2f2e308f51d8d7429e295b50eee33fde78d7150
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c977a996df7edb4727b1ff8309f31e21faaf268e
Author: vince <vebeckner@lbl.gov>
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 98f6938c38c423660ffdd5a7366912263fb82682
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:27:05 2015 -0700

    allow Intel compiler more memory and time

Tools/C_mk/Make.defs

commit c925bcdd1281baaada24edf9323a9baf2fbd6188
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:23:26 2015 -0700

    always use cray wrappers

Tools/C_mk/Make.Linux

commit 40049f04f4a279d90fe610823299298cbb920abe
Merge: 921e4bc ce2c315
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jul 12 22:22:09 2015 -0700

    Merge branch 'mempool'

commit ce2c315a68d947cc96855742b6ddaec8c8859219
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 921e4bc85b93187b4fc9df8d65e36ff309ab293d
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Jul 9 08:57:42 2015 -0700

    works on any babbage login node now

Tools/F_mk/GMakeMPI.mak

commit 1887cd78d79b93f6625497b01768fcc60bad7005
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 7 15:15:11 2015 -0700

    some cleanup.

Src/C_BaseLib/FabArray.H

commit 3fc6bafd9bc1379a63cfd46a04a886d7995a8087
Author: vince <vebeckner@lbl.gov>
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 51ec5bc17ad832ffd8185458af1b984490c1e58f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 62b07cd9cc6b04c8eb0e56d657403f9b0355c954
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 30 12:56:15 2015 -0400

    remove debugging prints

Tools/RegressionTesting/testnew.py

commit b5e14617fd64389aa9bac077a1bfa0ad1043611c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 30 12:55:27 2015 -0400

    catch AttributeError for the compilation failure too

Tools/RegressionTesting/testnew.py

commit 16f348309b39648fdd6f778e2b77054b5f377eae
Merge: 0b6e656 2802ea1
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Tue Jun 23 15:21:52 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0b6e6560e0759b3d55137ff00407618581c0693e
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 2802ea1263488d1b8c9651737fad77e392a9af5f
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 22 13:30:10 2015 -0700

    Changed path

Tools/F_mk/GMakeMPI.mak

commit a8ce9a1395826ef7b06d31d5782f9c6568a548a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 17:20:18 2015 -0700

    Add 3D UniformVelocity test.

Tools/RegressionTesting/BoxLib-tests.ini

commit 51ffe8e476aaf9102d0f196812c9518a60bc82bc
Merge: 6b04925 5be1510
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jun 18 17:19:23 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6b04925b493d79feb6c03ae3c124d4bd5d91d69d
Author: Ann Almgren <asalmgren@lbl.gov>
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 5be15104db5f9bb52d0ebd4d8f830bd1e7e4aa2f
Merge: ad0d658 3d537fe
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Thu Jun 18 14:31:16 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ad0d6581327d86e453df60947b5a2ce8989aece2
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Thu Jun 18 14:30:43 2015 -0700

    Turned off Intel compiler runtime warnings.

Tools/F_mk/comps/Linux_intel.mak

commit 3d537fe2f23c26b7a1cdc9a1491be693f85ceae1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7c244bda48c2be174997c92d8cc500752ae82b15
Merge: b182505 519d913
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 14:06:06 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b18250593195c7d4b592abdda167f4cdaed53ab4
Author: Ann Almgren <asalmgren@lbl.gov>
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 3fe36273cccbefe1ae4fce5947f90b571be12099
Author: Ann Almgren <asalmgren@lbl.gov>
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 df281fb441dede1e803d2f632d7b930d007ce6f2
Author: Ann Almgren <asalmgren@lbl.gov>
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 29b3df07d54979ae17540c0563bd6f636a102bbb
Author: Ann Almgren <asalmgren@lbl.gov>
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 5316ea4dc0d86dc447410eb1058e3b586b823e8f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 16 13:04:14 2015 -0700

    Remove print statement

Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit ba7cb79dbf9a92a1a354f2316c7524580a23849a
Author: Ann Almgren <asalmgren@lbl.gov>
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 519d9132f10be4a45719345f8a6ac4f0eb3ce810
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 89fa316f658cdc1456625c3b03d34c11ae04071c
Author: Ann Almgren <asalmgren@lbl.gov>
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 d3883a423d66f72e375f2f7a65865e4ba6fd4dda
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 15 17:10:58 2015 -0700

    Fixed various indexing errors.

Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90

commit 977b265e15489cb4137b808bd7da959a88618e97
Merge: 9e0c937 cbf205a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 15 13:17:36 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9e0c9374502afb8a564a08a435d013c62bd134e2
Author: vince <vebeckner@lbl.gov>
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 ca0dbc9d720c971e8194cc021a2daca842dec465
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 10 14:19:19 2015 -0700

    added id for distmaps.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit cbf205aa53d816e2235694adf08cc5a167ccb6ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:39:49 2015 -0700

    update the comments

Tutorials/Tiling_Heat_C/results/run-babbage.sh

commit 1cdfa03f1209b2cfe59b7d123e26be3bac9c7917
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:27:44 2015 -0700

    SMC: extra optimization flags for babbage

MiniApps/SMC/GNUmakefile

commit efea1b9840c56320d84ed92fbea091c456557f97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4c8e405f79232def461648c4cfabe65213349b8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jun 9 13:23:48 2015 -0700

    fixed a new 2D bug

Src/F_BaseLib/list_box.f90

commit 1243abf8af384e6967b414adb4f594b6bdb9bfcf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fd49b282b07a304138cc49c48c9fe4a18b552c9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aa265eff506596b9edeec6f4a9af3b5ab3aefa3d
Merge: 6ebb02e 7313a04
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Jun 8 13:16:22 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6ebb02e1858f170dde01e8b3d0843e6fad8f1b48
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7313a0444c79a5269db5649d5deac5bf6325a0b6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e8d7f9d4bbc35dd046c3b4afad0840c90f9a5a97
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b9da99ec7005c1813c251d8ca6237d95ef86471e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 14:36:58 2015 -0700

    Fortran mfiter: fixed nodal bug

Src/F_BaseLib/multifab_f.f90

commit 155581d393c72ccf2e531e5b794e581f2358734f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2b2d1af8f60b3c9f346dd994a922607e27ee4c87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b94c5aa0a7ea7622a009dfb6363f21e9c9e58330
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 10:33:47 2015 -0700

    tiling in Fortran multifab copy

Src/F_BaseLib/multifab_f.f90

commit 5379f99b092e6a98bc7230a5b053b312b4f782b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 10:11:19 2015 -0700

    Fortran mifter: fixed a bug and tiled setval

Src/F_BaseLib/multifab_f.f90

commit b058e92fb008f29db5a34124111114c4e66c6056
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 612fa19864979a34605ef3f7c80cf488a5ad7f8b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 7 07:56:45 2015 -0700

    Fortran mfiter: added optional argument, tiling

Src/F_BaseLib/multifab_f.f90

commit a14a5bf055f2e7b971a0e648201da7a885c34a5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a87fa0f0fc8ebe128f895f5fb00ed1ebfbb0a483
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9c0c170b44ac29f3cce79b32e0444423139732e2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5bd6b3474f445ec5a4f3b66b20b47b2b7f27a127
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jun 6 09:41:34 2015 -0700

    minor cleanup of mfiter

Src/F_BaseLib/multifab_f.f90

commit db79d9306c940dab44b2e1e81de90b7a8a471eff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7920e8d9c0725f43e63acdef16d7fe7525b178f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dd095be0e1a1435bcc855de7b9f82ae511b5d561
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 17:40:38 2015 -0700

    changed defaults

Src/C_BaseLib/FabArray.cpp
Tutorials/Tiling_Heat_C/inputs_3d

commit e95854e20f444e1322694d0e7fb1ffdce36ae939
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jun 3 12:11:52 2015 -0700

    removed an unnecessary std::max

Src/C_BaseLib/BoxList.cpp

commit a1378740da3f64dd53b80cc24ad4c4989abee377
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9abcff3203134392d9f4a383a674736afa7ab16b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a690fad4c6529c2540227d0ef655c8ca226f75fb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Jun 2 20:16:42 2015 -0400

    fix a bug with --single_tests pointed out by Ann

Tools/RegressionTesting/testnew.py

commit 647476b719534971b0afd2fb930c45d145806d3f
Merge: 6c08142 19d3b67
Author: Brian Friesen <bfriesen@lbl.gov>
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 19d3b67238d3406058b6a7a62b508566a47bd77f
Author: Brian Friesen <bfriesen@lbl.gov>
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 b50e0a40e7f8d873512d7c16532e287b7a7b810b
Author: Brian Friesen <bfriesen@lbl.gov>
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 cc36b06bc230f4a22270e6b38f446ebec0ce0396
Author: Brian Friesen <bfriesen@lbl.gov>
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 854777dbaa502cac5e6d87737edefbda886577cb
Author: Brian Friesen <bfriesen@lbl.gov>
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 6c081424e6c2f3577372805e1bf9ccb2d9544298
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon Jun 1 14:30:36 2015 -0700

    remove broken links in doc

Docs/GettingStarted/GettingStarted.tex

commit bc71cd8e8be4944ffa3ef657048f112e4d0540df
Merge: 286febe a130676
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 14:03:29 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 286febef36a1e9cd27e11dd9935a865efdb338c2
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 14:02:44 2015 -0700

    Fixed typos

Docs/GettingStarted/GettingStarted.tex

commit a13067672eda84a5ee30f102a24f5d72fa87112b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2bf9567a661119e0872b81b00e3926743016f197
Merge: cc3030f e251cb2
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 10:12:20 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cc3030f07af201a1a55c3a450c105a0b7e32da65
Author: Jessica Kawana <jkawana@lbl.gov>
Date:   Mon Jun 1 10:10:55 2015 -0700

    fixed a typo

Docs/GettingStarted/GettingStarted.tex

commit e251cb2a1efea41c8042ff6a931554bfbf31b071
Author: Ann Almgren <asalmgren@lbl.gov>
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 1513c6ec7525269500d9445d448a89f441b81f20
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 c302ddc7d4e1934314971386c3268927baabfad8
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 28 18:28:43 2015 -0700

    movegrid tests, random copy from movedgrid mf.

Tutorials/MultiFabTests_C/GridMoveTest.cpp

commit 97e7429b6fcab2db88fc579e3808631ee816d135
Author: vince <vebeckner@lbl.gov>
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 e9f5c60e39d2d9f277cddc33c6bc1bf439b32dd2
Merge: f665912 ad09dcc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun May 24 15:24:54 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f66591255c159d25991ad212bc9f7b7100a2f731
Author: Ann Almgren <asalmgren@lbl.gov>
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 f57828a8210870a9462fab3817729a265b8a69e4
Author: Ann Almgren <asalmgren@lbl.gov>
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 48b3404ea6ccbb956380584148f9506c19701734
Author: Ann Almgren <asalmgren@lbl.gov>
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 ad09dccebe07dde5b548117225cdb6da25350047
Author: Brian Friesen <bfriesen@lbl.gov>
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 dfb721ede7c805d65eb21a3b6bc3ae1da14b1600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e2c77bad6f456575cababab6be9becd20aa0f90b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 16:23:21 2015 -0700

    crayftn --> ftn, craycc --> cc

Tools/C_mk/Make.Linux

commit 64178d595cbca9f47c14fd9eae693c6ca2847346
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a53cca19db1ffb13de094331be16082b879b7f0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 315454c51703f9e2eeb649f27b6412767811abfd.

Tutorials/Tiling_Heat_C/advance_3d.f90

commit 315454c51703f9e2eeb649f27b6412767811abfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 da1effb675f37454bf7ce280fae4d0d38428dd51
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 22 12:31:39 2015 -0700

    default USE_MPI to FALSE

Tutorials/Tiling_Heat_C/GNUmakefile

commit 0fbe6727d9a2e0331e72a9404d883636f121c924
Author: Brian Friesen <bfriesen@lbl.gov>
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 8d188a880333f311f4874cd204705dcf6e11c7eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 21 14:14:18 2015 -0700

    change default compilers to Intel in makefile

Tutorials/Tiling_Heat_C/GNUmakefile

commit 8f31ff4250a1926259b7568a12fa1f45d3cd6353
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6ec1bdaaf16226eaf20cae9c2df79e6e3f90bf8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9b8eb069ded3f3b528e72d0e312f8656188aea4
Merge: ef3f17d 111fbfd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 19 17:45:34 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ef3f17dfe7f0b83c10fd180f6b9883938e428bfe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 111fbfd90ea242b0b289d3bb450e888f0e58a5ec
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 19 16:21:47 2015 -0700

    test performance of mkdir and rename.

Tests/MKDir/GNUmakefile
Tests/MKDir/MKDir.cpp

commit 14aab69438373b6e410f71a16abd35f9db414393
Author: vince <vebeckner@lbl.gov>
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 554f044945a445963e89db2e62cf9c799f08f6de
Merge: 9cc016f 7cf2824
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 19 15:58:56 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7cf282491f251827b3f4aa9e32e407116c0c4d77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 19 10:57:15 2015 -0700

    added -lmpichf90 to bluewaters.

Tools/C_mk/Make.mpi

commit edb4fd3a738305d5856ab010a071334a12d07d06
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 19 12:17:03 2015 -0400

    more cleaning

Tools/RegressionTesting/testnew.py

commit 644e747e2ac2731f5ea4eeb365ed05cc533d9db0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 19 10:27:24 2015 -0400

    return the compilatoin string in the build_f method

Tools/RegressionTesting/testnew.py

commit ddf434d8a391845975f34a140178475ff825f1bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 22:09:45 2015 -0400

    some pyflakes fixes

Tools/RegressionTesting/testnew.py

commit 2010ed3c963a2fe1ca6ff366e1e1a2b251422eec
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 4626e6a24d915fdf452cf33584a017dd277a1e55
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 18 21:09:15 2015 -0400

    rename classes to be more PEP-8-y

Tools/RegressionTesting/testnew.py

commit 31d8158aa8009b1e00879f4687363ced76a9a97e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ddd0f24053c7941ed9ac7eb4754fd3aa4d823393
Merge: 96acaf0 793376b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 18 14:52:55 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 96acaf0cb82a6b69c25088fa887f451b6300bc74
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 793376bcd2afe6eaa48bb7009ff10ab626e2b10f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d3b8c7a98fd0d71e5a720d4a2c9d484479ac1b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 13:06:00 2015 -0700

    fixed heat equation ex5

Tutorials/HeatEquation_EX5_F/main.f90

commit 6299f806676b067b4dfbdb17b53773543afc4390
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:55:46 2015 -0700

    quiet valgrind

Src/F_BaseLib/vector_i.f90

commit 918e575311bc91539bebc57d200dd227af26d67f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:54:56 2015 -0700

    comment

Tutorials/HeatEquation_EX4_F/main.f90

commit 95acf9cd301fd5a291dcde46bcbaa932adf65c41
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 18 12:32:00 2015 -0700

    Fill ghost cells if tagging needs ghost cells

Tutorials/HeatEquation_EX4_F/main.f90

commit 2f10f53d57b735633b5f932600ea44b302b5bf40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 76de0a013c1e6b09cf7181468ba07eea821f39a3
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 9cc016f4ed397fe74b94111f2e3447bd7b4de3f6
Merge: 025aa85 516b3ae
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 14 13:51:57 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a6e4f794e76afe9a785b76ef7c202b2c1e98df64
Author: Marc Day <MSDay@lbl.gov>
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 516b3ae6fc9db3abced62b14de437d01a1f6a66a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 60bf5905668822f8123a83b23f08f8f2d6a1c34b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 10:44:54 2015 -0400

    some more simplifications

Tools/RegressionTesting/testnew.py

commit e88cdc058918ca5fa88050f59d06301a52634198
Merge: 1effdb3 a44325f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 08:44:31 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1effdb3998db3e71aa75c619d62a7b1f205d7a51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri May 8 08:44:09 2015 -0400

    fix num_threads -> numthreads for pure OMP

Tools/RegressionTesting/testnew.py

commit a44325f64f1c63244b2c205fa5c58e8e98a9b6fc
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 20:03:30 2015 -0400

    fix the hydrostatic_adjust case

Tools/RegressionTesting/Castro-SBU-tests.ini

commit bd82028e14d3e5f1146dc9a1672a06712030aa35
Merge: 78d3db1 29245a1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu May 7 14:12:13 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 78d3db16ca6c27f91a27e70e43e0990990f53d00
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 29245a10a33cd8dcc6268ff3f8339eab22d3ee1e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 025aa858342af8f3fe8d41b1e669b55f60defe8f
Merge: 8b6bde7 fe2e663
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 6 17:33:17 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe2e663be90d32230a387df06fd9b7e3f1560ec3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed May 6 09:32:54 2015 -0400

    update the sub_chandra build location

Tools/RegressionTesting/Maestro-tests.ini

commit 4b403ffaaa71da7f28325a170d81453a99f5e84d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5974bed824b9a6ef2868f6541a7456d1344935f2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 19:21:23 2015 -0400

    more simplification of the run commands

Tools/RegressionTesting/testnew.py

commit 5eb08b2d29a3b1f0adb4354468482322aab1c2d1
Merge: af91910 51819bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 17:19:13 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit af91910c18f3836b562044c78f50928536d0195d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 17:18:53 2015 -0400

    remove redundant code

Tools/RegressionTesting/testnew.py

commit 51819bdad9fca5cf0cfb916f6355f83e8faa66a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 54a2e73eb68ae41b24b2aeb5f837dd0a92a7c2d5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 15:04:12 2015 -0400

    fix typo

Tools/RegressionTesting/testnew.py

commit 4c71c82b58b0df34693b4edf98124f974ea67010
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 14:59:00 2015 -0400

    some more cleaning / modernization

Tools/RegressionTesting/testnew.py

commit f1ebe9db26050c3ccb5698c1d1cee429e6f18df7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue May 5 14:13:42 2015 -0400

    some more modernization with list comprehensions

Tools/RegressionTesting/testnew.py

commit 0a6576cdcf6f112af7910058b0986f8f694bc6a2
Merge: b2d8d31 17300fa
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 4 20:43:20 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b2d8d31f75b449a86521726d437696163c199431
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon May 4 20:43:02 2015 -0400

    more systemCall -> run() replacement

Tools/RegressionTesting/testnew.py

commit 17300fa05730b387932d6c216ecc4f6615764303
Author: Marc Day <MSDay@lbl.gov>
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 7aa26fc5059fd5a25a50af5b2fb38dfb90f32c87
Merge: 267684f 3afd74b
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 4 14:58:04 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 267684fc91135f6d707d15a33fb89752e15cb58f
Author: vince <vebeckner@lbl.gov>
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 d07f855a1aa1219682b219041eb7d962d0c7b572
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 4 11:34:56 2015 -0700

    nostart option for var.

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 3afd74b5dcf73fd26cc0a770d5092e7d5e37b0a8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Mon May 4 08:05:47 2015 -0700

    f90 mpi on atragon

Tools/F_mk/GMakeMPI.mak

commit 7d4873e709c07277d5203d0acff27a9238e2b7d0
Author: vince <vebeckner@lbl.gov>
Date:   Fri May 1 15:05:34 2015 -0700

    removed buf size restriction in Concatenate.

Src/C_BaseLib/Utility.cpp

commit ab429bd6be23d10db34b224df0b1e77c363855be
Merge: 02b9acd 88e881b
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Fri May 1 15:35:09 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 02b9acd326cf2871f486378cf5fd5ad19986c73d
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 88e881b1572d463a0cd92ed3f3f31969491696a4
Merge: 1cc75c1 d6f5758
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 30 15:40:05 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1cc75c102c6150d4420a4dea3bf1f71d79706422
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 30 15:39:47 2015 -0700

    mpi on orga

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 8b6bde7dac859038c3329357f07a790ddb9dfcdc
Merge: 33f4c20 d6f5758
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 30 15:30:54 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d6f5758014d3285f87c654b73faf806a3a92a729
Author: vince <vebeckner@lbl.gov>
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 33f4c20e218ffff3cbfe72735f74562ea9322edb
Merge: b89095c 33c7336
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 28 16:51:14 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 33c7336ba7b50f88f2a56375dfa14cbc6afc25e8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 28 14:42:35 2015 -0700

    define BL_ALIGN_BYTE and BL_SIMD_LEN

Tools/C_mk/Make.defs

commit 0ae24ade5a7980e11828f661fb3817161bd4829a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 0959a3df858509c624cfa65469619d310d836c0c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 c6f22d90fb530c50bd8cb220e10f9acced14a57d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 dc677528873381f989e730e03f7d860e4d607e74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 26 11:17:45 2015 -0700

    add BL_ALIGN_? to make for array alignment

Tools/C_mk/Make.defs

commit 33f9902b41cdb793206e0967fdc55b9e905d4806
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc4b0e48478f6ac73aa7bda94cc4cff3581f2f14
Merge: f86151f d8df7db
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 22 17:21:18 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f86151f1fc9c0573148555ddba6c126c1ddd927d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 22 17:21:09 2015 -0700

    nesting fix.

Src/C_BaseLib/BLProfiler.cpp

commit d8df7db524a1baf726bd0580beb980cc45cea251
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 22 16:42:16 2015 -0700

    removed -target=linux for hopper

Tools/C_mk/Make.Linux

commit f4691440ab004a4f303ea93716bac6f580340b94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 35f7f3230804d02127a732fab7f29865362392e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 19:21:02 2015 -0400

    some more clean-ups

Tools/RegressionTesting/testnew.py

commit 2759a86211d07777b5931b8db38780ffb63cbd78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 25443a5c9b77dee0554efc90e932879ecc55b558
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b28c94f7a52161244af5e5902f7bed623e10299a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 f60dc17e639d443a62d038aef7bf1324a8971b32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 21 12:46:05 2015 -0400

    some more cleaning -- especially to the restart execution string

Tools/RegressionTesting/testnew.py

commit acd85262c8d52aa4c6bc08d614ec394a03ab1efa
Merge: 9f999bc 4552f32
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9f999bc4d4e7f85f3b672aeb22692ff87d38d5f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 4552f323dec6020ba4380e3a3a151575ae77ae6c
Merge: ebfe936 419f8e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 20 21:51:32 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ebfe9367b81c36fda5db4d0b8ac2a1467561fe17
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 419f8e692b77598b94db316482317700a444f664
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 20 20:20:37 2015 -0400

    remove some os.system() calls with shutil -- this is safer

Tools/RegressionTesting/testnew.py

commit c7bf2c8820c7814ff7051dc37b72e24de7c3c7dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Apr 20 16:55:28 2015 -0700

    changes OMP approach in FillPatchIterator

Src/C_AMRLib/AmrLevel.cpp

commit f5d83082d23f3d6b677eae720ba60d6b10784ebf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 20:36:32 2015 -0700

    tidy

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c

commit 550a5e80a3a475425793d8caf29267348fc1b4ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3bfdac3956f792ea68780760630ff378dc4fd58d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a4becda3c0cfea534c12a23258eaede231e4ff37
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 080df2a6ea761e605924e65ca12b1f6a0d0b0e39
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 94439f2ff2b603cdf2634151e9306d0992ac3cc6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Apr 19 14:24:16 2015 -0700

    typo in comment

Src/F_BaseLib/bl_types.f90

commit 2bff64d27f4fe535d27611d6cc606587a7d973f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b89095ca9e987d753839727d373451d001672951
Merge: 11e57ec b013071
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 16 15:21:38 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b013071c9b45885a043e077ba07aa275416c370f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 16 11:07:17 2015 -0700

    fix a print statement

Src/F_BaseLib/fab.f90

commit a099ee1097313e3bbd6c49ad7925d2f037aca776
Merge: d52fd1b 20520f9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 15 14:42:58 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d52fd1bea88860d4b506bb1d5166b2f785f7e5ca
Author: vince <vebeckner@lbl.gov>
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 11e57eccc19e8a321e06d1a4b31fa81d53958878
Merge: bb70cfe 20520f9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 15 10:36:00 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 20520f96eeeb35563f68405213b90e18e181cb5a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 0d11ae094fb70c1860f94be48847c24c99acea7b
Merge: 559ad2f 935df63
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 18:55:31 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 935df63f887c7b1d96cd3926e07a8aed421fff9a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 18:54:52 2015 -0400

    switch fboxinfo over to run()

Tools/RegressionTesting/testnew.py

commit 559ad2fb4e69cf504a04a277f22400dc2f8efe4f
Merge: 641d516 d9e8754
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 14:10:48 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 641d516251773a11dec3be1a1958dabd06b607f8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Apr 14 14:10:38 2015 -0400

    some more run()

Tools/RegressionTesting/testnew.py

commit d9e8754e5b8c87a3e86dd0f2caa42e4b5d7aa44a
Merge: c799bb3 56d8954
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 9 15:52:13 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 56d895444c640990f64abaa80d4554c7098233e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 8 11:45:56 2015 -0700

    clean up Intel's optimization reports

Tools/C_mk/Make.rules

commit d1167461683102f170c9fcd372359ee0d9d28d34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Apr 8 09:31:39 2015 -0700

    For Intel on Edison, add vectorization report

Tools/C_mk/Make.defs

commit 5274264304f994b19f729093b9cf17806731c6b3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Apr 7 12:37:35 2015 -0700

    save stdout and strerr of make in make.out

Tools/RegressionTesting/testnew.py

commit c799bb3aece7f6fe64a974299a61c47d17ead036
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 14:01:08 2015 -0700

    some perfmon cleanup.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 68e6423532122c665d096c31dd74205d1a1ec929
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 13:21:11 2015 -0700

    some cleanup for perfmon.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 26568227a2040c45785ca0422902b23adade072f
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 6 13:20:35 2015 -0700

    fix for serial.

Src/C_BaseLib/ParallelDescriptor.H

commit 884a98299f55f5d286fb20574da1093e682564cf
Merge: 9f021ad 6c8abf2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 6 10:25:27 2015 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9f021ad2b10183ed2b38d525af4d8fd4a1084c2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6c8abf2d63380fe5e5643e99de28ea7c2784587b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Apr 6 10:20:29 2015 -0400

    take another git hash directory to accomodate MICROPHYSICS_DIR

Tools/F_scripts/makebuildinfo.py

commit 6fea5eae07841d42555b854d1542a13c3e75b4e1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 55749a625a5974ad521249cd79d14665a556a3cb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 551041edb2a8c3a500bb6cdfb973964eb037c38c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 2 14:45:12 2015 -0700

    Uptick tagged version number

Tools/CMake/BoxLib_Version.cmake

commit cf034bebf40dda642ceb269292f453b2801dfbe0
Merge: 1783e2e fad4b15
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Apr 2 14:41:34 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c8ce73fb1de3ce7b37c4b6215babfbea40f6b348
Author: vince <vebeckner@lbl.gov>
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 c9d1d01398185b80f0c2a406fdb3adcacfbfdbb5
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 1 18:18:45 2015 -0700

    support for multiple perfmonproc processes.

Src/C_BaseLib/BLProfiler.cpp

commit fad4b157c0dc6f708f21d4c5e600e0592796c106
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 45cc74c4c2fa984831f467e0b32141c5dd745738
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e92f198afbf1d4f2af36b9ec3966e783c744ccbf
Author: Regression Tester account <regtester@battra.lbl.gov>
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 e8995767635f9929b69a04029869c048f36411bd
Author: Weiqun Zhang <WeiqunZhang@lbl.gov>
Date:   Thu Mar 26 11:05:25 2015 -0700

    updated makefile for battra

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 2ff86a93ef331de1371e2c8fe4c684d7452be76b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 25 11:48:43 2015 -0700

    added more profiling.

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 2d6307d007abed51bee75e93cd531dcb19d07890
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 25 11:47:52 2015 -0700

    checks for zero size arrays, percent for cov.

Src/C_BaseLib/BLProfiler.cpp

commit 9d09b7a4c0fedb839109d12d398cfab3b276f843
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 19 12:49:12 2015 -0700

    added coefficient of variation.

Src/C_BaseLib/BLProfiler.cpp

commit bb70cfe43c3669ec8120c5d6004e3c0b2cc06df5
Merge: 2e2a673 d94cc43
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:33:11 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d94cc43cd72e5c0a33f38ba939043e0fb64462a2
Merge: 4d94ec3 539cb40
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:31:19 2015 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4d94ec3be851c1da0012649de18ba77293de4f81
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 18 15:30:56 2015 -0700

    showpoint to avoid 0 parse.

Src/C_BaseLib/BLProfiler.cpp

commit 539cb4064c182b657d9bc4758aa781158a1a8f86
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 16 14:39:05 2015 -0500

    Update rules for Blue Waters compiling

Tools/F_mk/GMakeMPI.mak

commit 07f9e41482a0f9410df85b0c85702261f65e19a8
Merge: ddc3197 9c80caa
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Mar 16 13:04:53 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9d7fd6b8b801c85ee1241eea25d9baed849a33ca
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 12 17:43:27 2015 -0700

    makefile update.

Tests/IOBenchmark/GNUmakefile

commit 9c80caaaa45720e09a5fbda175c4f006cdd5117b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a786e8f1b72745307daa74eac11ab2755a5a819c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 30d8bdeb66755164ff79ebb454f68815bd82d9dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 12 17:14:52 2015 -0700

    increased buffer size for backtracing

Src/C_BaseLib/BLBackTrace.cpp

commit 7a011c8ee0722a9da1a3e322a341d3eb30026fd1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 1783e2ea8f8ec63ee1ceda5b47a8ca708dc1f968
Merge: deb1863 6a58f02
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 9 17:41:12 2015 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c2e82b06b5b12f7e6fc999b05f043d2e5ab0ac07
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 6 17:35:41 2015 -0800

    extra send interface with comm.

Src/C_BaseLib/ParallelDescriptor.H

commit 6a58f029f128c3d252f5ae3853a0dc387a8e39cf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 5 22:13:30 2015 -0800

    use range based for in Lazy

Src/C_BaseLib/Lazy.cpp

commit 33629cc6ee14561a10b07c885f50405e376b84ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 deb1863f1dfa207e988914012d4613ea3502ffe2
Merge: c8da6f0 aa1c247
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 5 14:17:01 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit aa1c24709fed9ea7e0d47eb5cedf3443aa83ab10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 28d682c31879146d2177f898dd1e5ed893351580
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8a10b50bd08d6741b23b7709d9d0eed1d21a6c6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8e790ebb548dc8d02f2a330672aefef2b5658589
Merge: 3a75883 7e2e3d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 17:20:06 2015 -0800

    Merge branch 'lazy'

commit 3a75883876bef2cccceca1631bd4244c112ac8e7
Merge: 3fc24fc 6be72b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 17:16:22 2015 -0800

    Merge branch 'lazy'

commit 7e2e3d3dceae00b65a833d555f024ee6d456ea91
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Mar 4 13:58:54 2015 -0800

    fixed it for Intel

Src/C_BaseLib/Lazy.H

commit 6be72b810b5356122f914d8bcf5597cbb892aab9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9bf26492062c003f0db1194cac8d591369a94909
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c8da6f0cc2f304c1ef3c80e6d939834b8f00fb8a
Merge: c6f9789 3fc24fc
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Mar 4 13:15:52 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ddc3197febe5d2f734eddc5a2ff34c94c9223dc3
Merge: 9aa54a9 3fc24fc
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 4 10:53:34 2015 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3fc24fc0adc453192f828899a26f3bedbeef9d22
Merge: a91e1fc a023226
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 3 12:46:16 2015 -0800

    commit merge.
    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a91e1fcc0a093d7b27707f1a3790be6f4550dc45
Author: vince <vebeckner@lbl.gov>
Date:   Tue Mar 3 12:46:06 2015 -0800

    update the profiling doc.

Docs/Readme.profiling

commit a023226e4ffffde266ef77be0b03f91875c07558
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Mar 3 09:39:02 2015 -0500

    update some problem locations

Tools/RegressionTesting/Maestro-tests.ini

commit c6f978975022a87073c346239d628e2a336dc59e
Merge: a0c4803 505c096
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 2 16:43:13 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a0c480319b075eb37927110fffefd17073f21357
Author: Marc Day <MSDay@lbl.gov>
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 505c096feea00a4985abc844d676dfb9ecf42039
Merge: 8b84ef6 1da3a2c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 2 11:59:47 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1da3a2c369b29b85b2606e59fc6baad562a01f7b
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Sat Feb 28 05:56:22 2015 -0800

    mpi on gamera

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 2e2a67307567f6a763cedfd6ccf93823326619c0
Merge: ffaeb61 8b84ef6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 27 15:33:46 2015 -0800

    rename dir test.
    Merge branch 'master' of naphta.lbl.gov:Development/BoxLib

commit 8b84ef608777814b0318d528d89a9db8086432da
Author: vince <vebeckner@lbl.gov>
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 f2124eb774c87418cfb1c85df09d4d8146d062a4
Author: Marc Day <MSDay@lbl.gov>
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 687f4dd42f31e5a5ef3bdfcc2a3cda24933a63a8
Merge: 465f51d 5db099f
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 27 12:49:51 2015 -0800

    Merge master

commit 5db099fa9ad5222bf02e55c16f1c609f57ce8f2c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Feb 26 14:25:36 2015 -0800

    minor change to slient compiler warning

Src/C_AMRLib/Particles.H

commit a36a04098d0dd6c6fa30bafa32622bc1fead9219
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Feb 25 16:13:53 2015 -0800

    mpi on battra

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 67b163aefdf9427a98ac168437c419c73e27fe3c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 24 09:23:07 2015 -0500

    a little more cleaning

Tools/RegressionTesting/testnew.py

commit 4101571a4fdfc8517cd567f407289a19e87abc24
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 5e7f9fe8c132aea2435014e344f07e9392e39dc9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Mon Feb 23 12:52:19 2015 -0500

    some more cleaning and PEP-8ing

Tools/RegressionTesting/testnew.py

commit 92254576dc98b641a3eee934f22e4d3ba80886c0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 dfcee6e2528b433cc34ac3907078dc09b63844fa
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 20 10:51:21 2015 -0800

    gimantis MPI for f90 boxlib

Tools/F_mk/GMakeMPI.mak

commit 460d306d7936f0d95c3895162237b0428da04fb5
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 20 10:36:20 2015 -0800

    changes for gimantis.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 3fcc394f2774d4dd80e974316327665672537eb5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:14:15 2015 -0500

    add some latex ignores

.gitignore

commit 4bc2946bda23f217590260a224bda871958b07b6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:08:49 2015 -0500

    remove stray }

Tools/C_scripts/makebuildinfo_C.py

commit c9141f75de8d9875f2f8ad858683656f1fe78df9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 18 10:06:20 2015 -0500

    update header with new functions

Tools/C_scripts/buildInfo.H

commit 6db0c2dc09b65579948531ee614db79b566e6024
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 b7c5e149434117b41a0534644a83258f8cd70b68
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 ea645f68c43a2baa75e6ac479c75cb1b7a3f19ae
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Feb 17 15:08:27 2015 -0800

    gigan MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 7ffd0f07e83e46400367dbcda980612aa8463204
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9bac157d9b56b68b90814e27f9659140d46eeb6e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 32d7bec71c67ef5f3831459e27a4b51a7fbad64f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 271bb7a185a76d3ae47bbe17d5ea2cb95ebc969e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 15:04:17 2015 -0500

    make BOXLIB_HOME relative

Tools/Postprocessing/F_Src/GNUmakefile

commit 2a43fcc5a514dd9cff62516a62499e05c8207e66
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:50:39 2015 -0500

    move these from AmrPostprocessing

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
F_Src/python/timestamp_02
F_Src/tutorial/GNUmakefile
F_Src/tutorial/fspeciesmass2d.f90
F_Src/tutorial/fwrite2d.f90
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
Tools/Postprocessing/F_Src/python/timestamp_02
Tools/Postprocessing/F_Src/tutorial/GNUmakefile
Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90
Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90

commit a33197ab5239adf03f75b65d0cd1199a74a0b9b6
Merge: 4e10716 b4d8030
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:49:31 2015 -0500

    Merge branch 'master' of /home/zingale/temp/AmrPostprocessing

commit b4d8030846736565aa6598ceeb808089817077e8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:47:12 2015 -0500

    moving

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
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
F_Src/python/timestamp_02
F_Src/tutorial/GNUmakefile
F_Src/tutorial/fspeciesmass2d.f90
F_Src/tutorial/fwrite2d.f90
GNUmakefile
MAESTRO_sub_chandra/GNUmakefile
MAESTRO_sub_chandra/fsubchandra.f90
MAESTRO_sub_chandra/fsubchandra_mod.f90
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/frates.f90
MAESTRO_xrb/fspec_total_mass.f90
MAESTRO_xrb/fspeciesmass.f90
Palette
faverage.f90
fboxinfo.f90
fcompare.f90
fextract.f90
fextrema.f90
ffdcompare.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
python/timestamp_02
tutorial/GNUmakefile
tutorial/fspeciesmass2d.f90
tutorial/fwrite2d.f90

commit 4e107169e5bd1b631fb19fd7b15d17067e126d0a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Feb 11 14:38:52 2015 -0500

    update to reflect mainline Sod_stellar

Tools/RegressionTesting/Castro-SBU-tests.ini

commit ffaeb61bd839dbabde672c48c749b33135a86f5b
Merge: afc15dd 995f4e7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 19:43:12 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit afc15dddfce907bd644d557b53d4fb9b26d66d13
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 995f4e759b756ce7e809678f39c82db656eb1faf
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 14:08:48 2015 -0500

    update for helmeos stuff

Tools/RegressionTesting/Castro-SBU-tests.ini

commit fb07c99075b41c2956a513ec821c4256171c64c5
Merge: 200c3cc 097dff2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Feb 10 14:01:23 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 200c3cc5d24512f6679689ed4a81d69ff38cc0bd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 097dff2880a13a0d657d1c19f4965296f0b2785b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e950fb2d5051f41457eb8d97c5f32a49820c20e6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 51019d89db5a1d6a3cb2fedabd69d6c858ec936a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d27af2c37ddce9f460f384de3224d39b31b06bfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 14:20:46 2015 -0800

    fixed typo

Docs/Readme.backtrace

commit 3099e7396323432afe825dc50c703255a41f7ca9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:59:12 2015 -0800

    updated Reame.backtrace

Docs/Readme.backtrace

commit c7b0717ea104a51a93334154e0d8986a39106d19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:48:55 2015 -0800

    updated Readme.backtrace

Docs/Readme.backtrace

commit 77dafebabebde51598f8a42c720f09b117e44264
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1dad9a515a11e4235cdc53aed875f426bb912a17
Merge: 3beed2d d304815
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 13:22:25 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d30481527789ece7442bfc6c8d33cd1378533c36
Author: Anuj Chaudhri <chaudhri@lbl.gov>
Date:   Fri Feb 6 10:33:19 2015 -0800

    Rodan MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 3beed2daab9af4f3e49b737482e68ea751441542
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 10:32:19 2015 -0800

    moved -rdynamic flag to LDFLAGS

Tools/C_mk/Make.defs

commit 2629e1868b0da4d8849f82b0d3ac9dfb0116724d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Feb 6 09:48:51 2015 -0800

    fixed multithreading in BLBackTrace

Src/C_BaseLib/BLBackTrace.cpp

commit 75d2da368a0a9f2046d35f164f7ea37479dee898
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 68dc5aa02c2c920ef6136d1546d22c9b48c37623
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Feb 5 13:21:25 2015 -0800

    mothra MPI

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 68fd21f040138d84ecc88ca7d497f24ec90999bb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 3561f185d12676111269548b7eb4d5928bb62b06
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 18ac531c130a65c5a7c233e069d87e3cdd293c51
Merge: f72b1ea ca8596b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 30 16:42:49 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f72b1ea8ebd8ba664e6e4bbfddb4fefd76610c0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ca8596b760fe828aad442d946e822a5a7b7a13b4
Merge: 27310bf e8f19d3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Jan 30 10:12:38 2015 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 27310bfdba51c06ed30d156a645a01c15476e9d2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e8f19d366bca7e8453110ad4485c8f65bb342e31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 29 17:06:00 2015 -0800

    removed some omp critical

Src/C_BaseLib/MultiFab.cpp

commit 0db952bacd126f1ce0a0b0c4a4b4c0080c1b4396
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 29 15:38:38 2015 -0800

    defs for new os.

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 851159f167b47ce16953bd93c9bd7c762893e8b2
Author: ajnonaka <AJNonaka@lbl.gov>
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 db55b6542bb891d0946e04e048b8662b5a51768d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ee15f1c1d50ced7b5ab4161b14f3a08d235b3185
Author: Marc Day <MSDay@lbl.gov>
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 a235af87d30cbfc721d4d7eb4da9b8daadeded7d
Merge: 34b16c0 271a387
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jan 28 13:53:17 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 34b16c06168a82bb3ae6e27a964b1a2bbef882b8
Author: Matthew Emmett <memmett@gmail.com>
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 271a3875426c0a1ee5cfa7e186937474b4d278b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 28 12:45:41 2015 -0800

    fixed assertion

Src/F_BaseLib/multifab_f.f90

commit 8ccce3c12cfb8b593b1460a613c34b5163d31187
Merge: 5c85b0b 9eea1d2
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jan 28 12:33:40 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9eea1d2234fe480a014f7c2c80dcf26bc8180556
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 27 22:13:31 2015 -0800

    fixed a bug in my last commit

Src/C_BaseLib/FabArray.cpp

commit 408e31a5cf7cddb0795b30ad2a37c5a0054e6bfb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2d1d278da186ae8a3c137b1484d5dc6733b44923
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 26 10:35:41 2015 -0800

    set the type of nodaltilebox correctly to satisfy assertions

Src/C_BaseLib/FabArray.cpp

commit dd751f2a09997c93edcbb8ab360a5f26e5d9d109
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 da72c4f947c699fb3e42d6a34af349608b43c825
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:47:15 2015 -0800

    converted to tiling in two places

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 43e653b8e6bc162a9b374a67e0b851f24b11b708
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:09:26 2015 -0800

    removed an extra endif

Tools/C_mk/Make.mpi

commit d0eacd01e789b4ee4b73ec78b089f31241286605
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 23 10:04:43 2015 -0800

    take a shortcut in make_particle_dmap

Src/C_AMRLib/AmrLevel.cpp

commit d0178cee85ecd85d0bc1ec862addf9c6d37cac35
Author: Ann Almgren <asalmgren@lbl.gov>
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 f587f2653eabf1f1304dd0b860a362762310db8a
Merge: 543f44a 4345904
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 21 13:54:09 2015 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 543f44ada49b793d9b575c0a8965ef77e1be249e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 434590420e956d7f9e5ab005593a6062685ab032
Author: ajnonaka <AJNonaka@lbl.gov>
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 6001ac7a11b1703c1a017c62464b1017bc113989
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 46360541e1f6f69ad3c834bffc8cd226ee445a5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2886b5be7c76c4fffabf333fa660aec646c78f9f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jan 18 11:57:07 2015 -0800

    merged RRKS into KnapSack

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 27d61977113dc31771830b32aa5d79d6de8a87f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 17:06:30 2015 -0800

    print put the number of particles too

Src/C_AMRLib/Particles.H

commit baa9b948612ddb9ce796288296cd33ddf5a68544
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 16:36:19 2015 -0800

    fixed a typo

Src/C_BaseLib/DistributionMapping.cpp

commit c4402137b46f6aa7ee9d7cbd80d0f4118e2a33a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 28ff0ef76edb9102d62d001690c14b3f83bebb31
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 13:41:41 2015 -0800

    fixed a bug in regression test script

Tools/RegressionTesting/testnew.py

commit 67e2b82b9c6715bb602ddcbfbdfd3c7e149ca103
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 15 12:57:37 2015 -0800

    regression test: link file can be a directory

Tools/RegressionTesting/testnew.py

commit c8aac4125cbff7f99f7849d5983147ac13354e52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:52:16 2015 -0800

    single quote to double

Src/C_AMRLib/Particles.H

commit 718c57256eb5a799542aba0c44ac62e9ba26d022
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ad512a17fe49f41df577d8e9e233a6d2f427b927
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 20:49:41 2015 -0800

    added extra \n

Src/C_AMRLib/Particles.H

commit 2078ff0041bfa91a054d8d67d6f236cbeccc96fd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a619d9b88052bf6c79074d1d3ac9d66449783b84
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 722f6e63c8f01329dc0b0023817d6812e10eadd7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 14 09:59:55 2015 -0800

    fixed typo

Src/C_AMRLib/MLSDCAmrEncap.cpp

commit b6976cb11e073a6aed282a362ac3881d679c0ce8
Merge: 0bf873b 781bd8a
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 13 15:01:07 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 781bd8a4b8713bad89e4fffa8fda18190fb2bbc3
Merge: 2473669 63e8d34
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 14:57:19 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 247366944b485235b226009a256e4114174c9b66
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 14:57:11 2015 -0800

    more openmp

Src/C_AMRLib/TagBox.cpp
Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 63e8d34cf204e8cd42e3fa87dfc6d3f4146a01ef
Merge: 49f4fd2 4f42509
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 13 13:23:10 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 49f4fd2ea0eebcee022fc896721e409222ac3437
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 4f4250930c46056967cef22ced9f573a7c7a2e7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 13:04:11 2015 -0800

    fixed typo

Src/C_BaseLib/iMultiFab.cpp

commit 0e92c6e8dea4ee1b3ca3b8cc0df77003a891ae6a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 13:01:40 2015 -0800

    added OMP to iMultiFab::min, max, and norm

Src/C_BaseLib/iMultiFab.cpp

commit ffaf6f8f281b1a6b4ea278c42290d9138a7e10df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 12:48:19 2015 -0800

    fixed new bugs

Src/C_BaseLib/MultiFab.cpp
Src/C_BaseLib/iMultiFab.cpp

commit 350c12d39261893278342b7c76cc1e717e5beb94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 13 12:41:54 2015 -0800

    fixed a new bug

Src/C_BaseLib/MultiFab.cpp

commit 58a0df604e74f50994e990d99f585918f5c40632
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9e2f2bbda103dcd047b9232ee22c771b63df869b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 15:28:01 2015 -0800

    removed an unstarted BL Profiler

Src/LinearSolvers/F_MG/ml_cc.f90

commit 0bf873b1a46d1b1c9d79cab6013738bc73e310b0
Merge: 31efce2 d083c80
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:50:09 2015 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 31efce2fa11f70fee638427b26fbade58382e04a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:49:48 2015 -0800

    test code.

Tests/C_BaseLib/TPROFILER.F
Tests/C_BaseLib/tProfiler.cpp

commit 92983d7e63a337cd03e0d551650a17fed6b6eefe
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jan 12 14:49:01 2015 -0800

    trace optimizations, flushing

Src/C_BaseLib/BLProfiler.H
Src/C_BaseLib/BLProfiler.cpp

commit 4fa8733fe9f220c7906fd0740f65771d7de6deda
Author: vince <vebeckner@lbl.gov>
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 d083c805028d22ef08fa0fa413003925bf59f4af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 14:42:30 2015 -0800

    fixed an unmatched profiler

Src/LinearSolvers/F_MG/ml_cc.f90

commit bb7b9708124997fcbc46f0991dc36422f8847b5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6bee71cc9bee209cec6c1280742baa8213826302
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 12 10:27:53 2015 -0800

    commented out BL_PROFILE in BoxArray::intersections

Src/C_BaseLib/BoxArray.cpp

commit 5b51623a070c2d160d398135ceb594a42933cab4
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Jan 10 12:33:56 2015 -0500

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit a9dea1316fd267ded2700e84ab43b5375ed3b720
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b35a7d0d7083db3faea5e5b8f36096b3a86b3b60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2b7bd3711f5cc0df3db741cce44ae642436e780f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 15:39:32 2015 -0800

    If CRSEGRNDOMP is defined, tile AmrLevel::derive.

Src/C_AMRLib/AmrLevel.cpp

commit 150db205e154481984a3f941032a9664326426a3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5f6c97ecfc530e021f7a8b6e6e05d0b55d280ce8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 9 15:06:19 2015 -0800

    use the new FillPatch function

Src/C_AMRLib/AmrLevel.cpp

commit c1e2cfdbf2e6db06a3c1fbd5ca874d297ce02843
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 12a95d0f6f35ac9565e78757a9745489d55df555
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 8 13:36:37 2015 -0800

    fixed new bug

Src/C_AMRLib/TagBox.cpp

commit d8de0faf5a37b8701f578bb57274521332d00402
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ca6ec0412e549dbb296f3123c39893ea7af7f5f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 6 12:22:04 2015 -0800

    fixed a bug I introduced two weeks ago

Src/C_AMRLib/Particles.cpp

commit fa0027cc224c6ffc93e85b822bdf52a0c2b691b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 5 21:32:07 2015 -0800

    added an assertion

Src/C_AMRLib/AmrLevel.cpp

commit 14e97f649813e66f32d62cf0e28d33cd2b75feff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f4fe13956c48b67c35ec7ea5df40c26e31a7890
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1f56c8ddc474f4d6a39cdf682a67cad620008394
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 90691c3cbf52bc4003b069ebc49c1dde9950bd64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7824e7aac44826115b09864851a1b602a5a85284
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1e216e469a0dd6d91d54015997e00ba3895455ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 20:36:45 2014 -0800

    fixed a new bug

Src/C_BoundaryLib/FabSet.cpp

commit f47ccf0f1aad0fc0089e2dfb69b0f1c8e3824e1c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Dec 28 16:00:29 2014 -0800

    added OMP to MGT_Solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit dcac0c0840bbe7791b6f3298037b77686732129b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2a39a1118d454c146d0a548e6a20703f9ae4f7f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ae6da048d55e2810fdd63be41d61406f06e5f62d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 36a2f8e6bec380864d00baf319e3e4e9b5eb9dfc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 23 14:12:42 2014 -0800

    removed an unintended nested OMP parallel region

Src/C_BaseLib/MultiFab.cpp

commit 3056d1391d7a4b0edb98b9204892d954aed417f8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 729854ed53b0b9d315b91273234fcb0e0fa5d35b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cc5465687732946e1c012a867ce9cbacc06fd046
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 20:06:25 2014 -0800

    minor shortcuts

Src/F_BaseLib/layout.f90

commit 18d793582bcaddfc6ca09a21be092613d8935545
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 90d9c7507853fb062c8d7ab94832e2b65e26eebe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 15:50:33 2014 -0800

    fixed a new bug

Src/F_BaseLib/layout.f90

commit 3f47844b32bda69523af2abee5419d040c9e7ca1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b1348fed1c6b99d00c727d02e83dceccf0569feb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 86d544e75e458cbed4f7bd189fedd26426baba20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b4a68f24e49b3d7ee12a1c0bc0262941ece70c23
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 22 11:14:00 2014 -0800

    OMP in SumBoundary

Src/C_BaseLib/Geometry.cpp
Src/C_BaseLib/MultiFab.cpp

commit 8aba9ac218ee01847281aba22eca3d20f78966ad
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 44c848f812eeca47403c851b1550c3c8c2ccf241
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 19 11:53:17 2014 -0800

    moved memory allocation out of OMP parallel region

Src/C_AMRLib/AmrLevel.cpp

commit b756778325f858718fb7dda533b656515cc5d772
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8731185fef12c9b38a7ff70774e5c0e2d4f68753
Merge: 2f08b1f 0c11ec2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 18 11:23:53 2014 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2f08b1fae8dd7abb3656add7ab7f441be3f05559
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 18 11:23:50 2014 -0800

    added timers

Src/C_BaseLib/FabArray.cpp

commit 0c11ec21345d1dc607d8cf0defceee037dc4deb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9eebb72abb847077f2141b3b44922fb4fcd515e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 15:06:57 2014 -0800

    OMP parallel copy

Src/C_BaseLib/FabArray.H

commit 51a873615777273e0b313e23b8c4eff0063665d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 13:57:52 2014 -0800

    more OMP in FillPeriodicBoundary

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 12b44e6157669f1b8fed5355008d27b54aaa2dc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 13:05:40 2014 -0800

    added OMP to FillPeriodicBoundary

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 6e919d149ee9963ddcd9c8ccf8c13cfef07a6c4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 258f7ad577fb5c1563495a6a62d37a641cdfb697
Merge: 78312a4 3e090df
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 10:38:41 2014 -0800

    Merge branch 'master' into commopt

commit 78312a44598e3eaec754c6be21b2e02ef3c2ab1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Dec 17 10:37:53 2014 -0800

    more OMP in FillBoundary

Src/C_BaseLib/FabArray.H

commit 3e090df7cf883e218b692815e79dd898aaab86a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bca2609e5869ca08b4cad8b017c53008abda9828
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 16 17:20:10 2014 -0800

    typo.

Src/C_BaseLib/BLProfiler.cpp

commit e85c1bbe0b7ac5b623276ddde7467c949c49f035
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 14:24:59 2014 -0800

    OMP two loops in FillBoundary

Src/C_BaseLib/FabArray.H

commit 699e72b1332f1c31401e8be37388d2b3df0f6eaf
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 16 13:42:48 2014 -0800

    array size.

Src/C_BaseLib/BLProfiler.cpp

commit 0884cfd6c4c4f9c99856f598ec6f29cb423f79c2
Merge: 01a6089 83c10c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 12:35:02 2014 -0800

    Merge branch 'master' into commopt

commit 83c10c3c45679db041cc96e3c23c5b79a9396a6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aecb88cc2b8db590c514f17cd5685749cf640cc7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 01a608933c2d8b227a005730b787c0cb4c7e7c69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 16 09:51:37 2014 -0800

    minor

Src/C_BaseLib/FabArray.cpp

commit edf539ea66b048a0d7ac0c8253152c3bfc70a600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a2cb52d3e74317bfda5fd34f952aaa5adc29f43e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 16940f74f4e80d17b35f8e6a5ca8892246fa4330
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 12 13:58:04 2014 -0800

    fix for sqrt, ioproc parens.

Src/C_BaseLib/BLProfiler.cpp

commit e358df5b1f6a26ab885fba2d714b06f5b63119f6
Merge: ab33f63 d84361b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 12 11:56:31 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ab33f63b0bb92c66ee7bea1901ad1856ae5cd51a
Author: vince <vebeckner@lbl.gov>
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 d84361b63bc23e67b9de17819e8bba1ba907a377
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 11 17:25:07 2014 -0800

    reverted my last change because it created new problems

Tools/C_mk/Make.defs

commit e1fcc42138a5861f64502ef2231465b507385245
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 67c94c42dcf41301572177f284bb2259aa99439b
Author: vince <vebeckner@lbl.gov>
Date:   Thu Dec 11 11:04:02 2014 -0800

    another donev machine.

Tools/C_mk/Make.defs

commit 9ee28b56cde48071dec3b0080562edbea6af80ff
Author: vince <vebeckner@lbl.gov>
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/Profiler.H
Src/C_BaseLib/Profiler.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 38d7375179a18264c46b12be0a6fca4a881825dc
Merge: 5b6e71a a4b0a0c
Author: vince <vebeckner@lbl.gov>
Date:   Tue Dec 9 14:33:23 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5b6e71a5d09e3900258ca1a2fab1421541230552
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 8 16:59:41 2014 -0800

    added more statistics.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit a4b0a0cf9f9c5716b00a226f1e72c74c223ce7fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 13:05:57 2014 -0800

    fixed 2 new errors

Src/C_AMRLib/Particles.cpp

commit 782e47e953977be22810b10821560a572d00fd54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Dec 5 13:03:18 2014 -0800

    fixed a new error

Src/C_AMRLib/Particles.H

commit 1f571643bae2d34cf53e00145034fd353b6d5d9b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8731e85444fa40242d8ab88e491b5aac0c7c292a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 171196b707bea9d16329c080ca11b86d7910e4b2
Merge: 7b15734 5729afa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 4 21:55:58 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7b15734f3015f791a0a0b4b001dc99d905071b67
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5729afa918fc3e30763070d16550f7b0848dbb3b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 4 06:13:04 2014 -0800

    added -lquadmath for gcc 4.9

Tools/C_mk/Make.Linux

commit 0262c2df8d6a2299ed42559e33a64e77f37965b9
Merge: df633b2 51c8c46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 21:15:44 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit df633b2b2e699e0f17415d565e1a385ffc5aa41d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 51c8c46f14c15b06bb06c1307e2b1e5280866b78
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 16:58:22 2014 -0800

    OMP'd part of FabArray::copy

Src/C_BaseLib/FabArray.H

commit 617649f65877a224f07fd74d600f7f58272290bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 16:21:51 2014 -0800

    added a timer to BoxArray::intersections

Src/C_BaseLib/BoxArray.cpp

commit 2062982d1a69f4904fe9a7e921c7f559bce01182
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:59:41 2014 -0800

    added a timer to FabArray::copy from a Fab

Src/C_BaseLib/FabArray.H

commit 76985033759daa729d559324dbdc2e48e0660005
Merge: 40ebd9e 7c6136d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:44:39 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 40ebd9eee387d0910bc938ca0d5b750218176500
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 74d8b7bb95d5e4e5690ac6be94a3567e355a7683
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bf6b07fd247dd8edb61690816239d990081d5047
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:25:13 2014 -0800

    cleanup

Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 459b50f181fef59f62f7695c3c4fbb8970daa42b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 15:05:31 2014 -0800

    tiled MultiFab::contains_inf and contains_nan

Src/C_BaseLib/MultiFab.cpp

commit aadb8abe1bc8c7afa383b2ca4b0dc7d3421f4569
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9133dc02563685a157cd28004351f637a0ddc6c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7c6136db438d5f3febcad0b8df61bd9beaf1f621
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 12:31:25 2014 -0800

    minor

Src/C_BaseLib/BaseFab.H

commit b871d80fb80e174f20001055fd3737983cc92894
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 2 12:04:53 2014 -0800

    tiled setVal

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit d58a8c8827785e47e4a6c5c76cf0ac5ad440d40c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fabf904842684b5a76547c5d0ff09e3f13c40a25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 af6b7d131edda1db8986ffb167d5f613113d4d3e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 17183ca8d75fdb4248715fa03d3611106705bdcd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e88fc3bbe0962c9c249e620e9e065cdb15f94142
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 15:16:36 2014 -0800

    fixed a new bug

Src/LinearSolvers/C_CellMG/ABec_2D.F

commit 8b673f03b8f3cfe0caac6367a12cc8ccc017c324
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 04f0024e2bdf0349921b45d86da1958d76d3a9cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 1 14:56:16 2014 -0800

    added fluxbox to MFIter

Src/C_BaseLib/FabArray.H

commit 97d2b921b270edfdda0a890f1b29f36930122391
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 28 14:39:54 2014 -0800

    BLMap: tidy

Src/C_BaseLib/BLMap.H

commit 50e9ea7f0dc243277d89ba427d73e02df3bdf961
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 be3d9d36f2cf190a3dff95e8f6f66a5ee16a5840
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:30:56 2014 -0800

    comments

Src/C_BaseLib/BLMap.H

commit 8fc65bf7f9d6bc427f3aa11148994ce60b1dbb18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:22:39 2014 -0800

    comments

Src/C_BaseLib/BLMap.H

commit cf0c63e0a280462b7bd93daf6dfdadfa03c42414
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 27 23:16:53 2014 -0800

    added more comments

Src/C_BaseLib/BLMap.H

commit a9453dd308332240192cf07347dcee82b21bbe7b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3158500407ee451a73120ba4a3e71f15622850b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 26 20:47:49 2014 -0800

    use std::lower_bound in local index search

Src/C_BaseLib/FabArray.H

commit 1b53e94e0b84239bb187436d164c1f75546cf6c0
Author: ajnonaka <AJNonaka@lbl.gov>
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 fab9bacbefeb2a167b32a46fc9fd5e03dec722a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7bae0fb7a7a1d25f0da2b34e00e25555feeadacb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 25 13:41:23 2014 -0800

    Add profiling to particle moveKick and moveKickDrift routines.

Src/C_AMRLib/Particles.H

commit cc9514c258a9e17c8e4a5ca7c4019963b598781a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d2f4f92a4c7ba7b03e09e3e27a01517894c545ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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
Src/Python/src/boxlib_wrap_2.cpp
Src/Python/src/boxlib_wrap_3.cpp
Src/Python/swig/boxlib.i

commit a77ce5091b4db713e9957e2d6deb74147ac6ed0a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c5b1467d98a9c6956b8706daa0287e26bd963827
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 23 20:43:47 2014 -0800

    adde an omp atomic to fix a race condition

Src/C_BaseLib/BaseFab.H

commit b0f3dc0f465e3540371bf582066de1662f4fdf6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Nov 23 14:52:54 2014 -0800

    clean up

Src/C_BaseLib/FabArray.H

commit 58406cf88a1a21259c294f24afebaba181ebf155
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Nov 22 22:07:02 2014 -0800

    use binary search for local index

Src/C_BaseLib/FabArray.H

commit 0f197ab47bab62143a34f3b5fa7c27350fc4d7f1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f027e228bcb7fb64afe189d7015742d08f128558
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6824111f1a11f719f541ea436d1e3b5d57b541dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 22:10:07 2014 -0800

    fixed another new bug

Src/C_AMRLib/TagBox.cpp

commit d75c10ed5be6680e549f47360b1959c955f0fc49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 21:01:51 2014 -0800

    fixed a new bug

Src/C_AMRLib/AmrLevel.H

commit 40ac1b0d4883dd181ffc2ef046631b19910493b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ff99c3d7a922380b931cd68b0d7332c1f6a6ab60
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6d37ad94b5ca7196800feae4d6b3bd3452fae245
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dadd93badd192f60e32630d974100a06ffabba3a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 57e3776b305e98dfe8a6a858315721c88c6ca5de.

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 ee0cb34713b0c8ede60a6f83829844cc417a1ea5
Merge: 57e3776 3ea94ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 21 11:29:32 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3ea94eecb0fdab90cb4cfc783902ff8a51d5565f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 21 11:19:23 2014 -0800

    removed some debugging output.

Src/C_BaseLib/DistributionMapping.cpp

commit d4f16ed653e6b8df59787a08d8b9244fd2ab4f0b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 21 11:11:48 2014 -0800

    removed unused vars.

Src/C_BaseLib/DistributionMapping.cpp

commit 57e3776b305e98dfe8a6a858315721c88c6ca5de
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b0c6b9d7bb37a8a46625964f381123489a32bf95
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d5268cc3b72b10c2393af654f6708b777c933e6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 683b77907012921082ffb28bf9e45cff8964700e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b547b411f3087b68531b87bc20217674bada3624
Merge: ccc7a29 faff396
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 20 17:23:35 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ccc7a299a24c7f096454456eb4951712d6fbd481
Author: vince <vebeckner@lbl.gov>
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 faff396e9ff672123f871a1df044fa49345c66e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 20 13:01:32 2014 -0800

    validbox in MFIter must have the correct indexing type

Src/C_BaseLib/FabArray.H

commit 465f51d7fe6ff821ca2dde079f8d945d5d77134f
Merge: 8db8e9e 5d5c1dc
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Nov 20 10:39:49 2014 -0800

    Merge branch 'master' into 4thOrderMG

commit 5d5c1dcdb744ceaed9d33eaeb428c85a1237090c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8db8e9e785f6e6e6f5e097c64bbabf20bb39ce6c
Author: Marc Day <MSDay@lbl.gov>
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 035e96eb82b52d9535cc6404801f32153091706e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f05a9305ecba802085a3bcc634b6817b7ccf0f4a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 16:19:10 2014 -0800

    commented out a cout

Src/C_BaseLib/DistributionMapping.cpp

commit f876859a2be417160ddbdc5f8cd1abe71dc8eb7f
Author: vince <vebeckner@lbl.gov>
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 223fb9776100efe49f88dd7859a988654f10af4c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Nov 19 14:48:54 2014 -0800

    added to the docs.

Docs/Readme.profiling

commit aa040a67ce6f21d7a9f3c4815c838c20f1c997e8
Merge: 42f7b23 dcbf1d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 42f7b239fcdeeeb6665cf457fe060c439530774e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 13:19:46 2014 -0800

    Tutorials/HelloWorld_C: changed domain size

Tutorials/HelloWorld_C/main.cpp

commit 474ca0cd27e8dad3b3317c941c21625efccaa8d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 19 09:30:41 2014 -0800

    removed an unused variable

Src/C_BaseLib/threadbox.f90

commit dcbf1d8df20b79eb24f14a614f6962214e1adedc
Merge: fb6721f c08554b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 14:28:02 2014 -0800

    more merge cleanup.

commit fb6721f6f61185837643d6e959f30dc78aa0c412
Merge: 105a386 9b5b6a8
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 14:12:31 2014 -0800

    merge resolution.

commit d14c972dc3091c7e3ce03eba4cd426e76a0e3ef0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 18 13:57:54 2014 -0800

    minor

Src/C_BaseLib/DistributionMapping.cpp

commit c08554b28f3ec53ae3c1e86e8b4dde561de14249
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 01795d3f2a5969cedfc9aa84b0daeee6f40deecd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 105a386579446d3f0987e56244d3d83f4c448ecf
Author: vince <vebeckner@lbl.gov>
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 246687a6e6054f4809ff2bc1b5e61148e6dd0978
Author: vince <vebeckner@lbl.gov>
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 29fca8e45a1502d3bb93c3dd2ea7e7ef3f4dc9a3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 18 10:22:21 2014 -0800

    some cleanup before the merge.

Src/C_AMRLib/Amr.cpp

commit 99041f8b836079bd9e68cdb8ca8e7df1cf50c9f5
Author: vince <vebeckner@lbl.gov>
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 9b5b6a88636c447c02db59183f180692413da9d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 38b5b1a95f4d1a76eb06c67f60f55a740386ef16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3ddd286d3726c3cf2b89b02e93caff688267a049
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c8aef11a9ae58ec1f2758df917797a05fa50772
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 15:17:51 2014 -0800

    comment

Src/C_BaseLib/DistributionMapping.H

commit 545c6a3e872b74be8dc86124115e921dc7829019
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c77dbaabc2566d98fc5bbfe8433357afb649d0e
Merge: 0ea96e6 cd402d5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 12:07:35 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0ea96e6606ce9a59cb84232a8024e9a55b4f12d3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d2a1767545f637f81fb80ce9895dd50a6b1681f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 17 11:04:59 2014 -0800

    minor cleanup

Src/C_BaseLib/Box.H

commit f4b1e81cfb0b86ff539ca359b2424dc970dea95d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3a3843adfc8a8e09cc84110b38ee4342a94f7454
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 14 13:25:07 2014 -0800

    modified comment

Src/C_BaseLib/Pointers.H

commit 5d2590547bcc18ed5dd9da28a78513adcc9a34e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 73f912357342dbe0f58a05664d28f106ef4b3f25
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 13 16:29:13 2014 -0800

    removed an old obsolete file

Src/C_BaseLib/std/limits

commit 5fb46d4995ff74a97a0803e4fe008c44da37f743
Author: Matthew Emmett <mwemmett@lbl.gov>
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/test.py
Src/Python/F90/tests/regrid.py

commit e1afb4a0e4579669e1140df71317562fc202094b
Author: Matthew Emmett <mwemmett@lbl.gov>
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 5656433e56b36bcad8658cc5485a179cea7d0b84
Author: Matthew Emmett <mwemmett@lbl.gov>
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 a412db953a38ce26b0c49f9bf21e311b77958103
Author: Matthew Emmett <mwemmett@lbl.gov>
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 c6db4e20aeea61205dfcada904cc962d98b657c4
Author: Matthew Emmett <mwemmett@lbl.gov>
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 0f129b657dbb09fee1bef0e267a0f7d65692391f
Author: Matthew Emmett <mwemmett@lbl.gov>
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 7626eea0f7b1b729255af4f6860b67b93804cdc2
Author: Matthew Emmett <mwemmett@lbl.gov>
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 397f8e21d5ff484aa5babc5ea821c23d9f9599ca
Author: Matthew Emmett <mwemmett@lbl.gov>
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 f3e389f5161b7f3c716f4336ad9e1a4397085b22
Author: Matthew Emmett <mwemmett@lbl.gov>
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 63d7a7a193f3629a126ea160793b0233678bbe1b
Author: vince <vebeckner@lbl.gov>
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 1c1c345ee13a83d76eaf21b95debdea093648871
Merge: 21d5ebe 6bccf4f
Author: vince <vebeckner@lbl.gov>
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 21d5ebe1898bacfb285cd5c7747e09f488d7ac6c
Author: vince <vebeckner@lbl.gov>
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 6bccf4f5f6987584fa7227057cc8f396520aa989
Author: Matthew Emmett <mwemmett@lbl.gov>
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 4feca5fd7292c1ee15a33a6f54e4dffda3444359
Author: Matthew Emmett <mwemmett@lbl.gov>
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 efdbaa3f5e4ee6bd962a1e7f9f90660674190641
Merge: 09eb199 3332fc2
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Nov 12 17:21:10 2014 +0300

    Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib

commit 09eb199310c89aad276146860659eb351c798eb7
Author: Matthew Emmett <mwemmett@lbl.gov>
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 3332fc22127517c63a17d8e264caacdc9360442e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 604d5f57513c2b6fd4027f8ea7a04224937cc6af
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c3f75972a0caa56df266c450eb3eff0cbaf28dd5
Author: Matthew Emmett <mwemmett@lbl.gov>
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 743096788d200afe20c25d8bf7f421601508924d
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 16:11:47 2014 +0300

    PyBoxLib: Another fix for libgfortran.

Src/Python/GNUmakefile_CXX.mak

commit fdf0b26be5b5e0a54d13c38cbc880f3da5ae2fe0
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 09:58:08 2014 +0300

    PyBoxLib: Better gfortran detection (from Aron Ahmedia).

Src/Python/GNUmakefile_CXX.mak

commit cd550e54a678373beea34a702c0e582af8dd2bcf
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Nov 11 09:57:21 2014 +0300

    PyBoxLib: Revert back to distutils instead of setuptools.

Src/Python/setup.py

commit 9abcfa56867347305f3a0ad9674fb5ae1ec98ef6
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Sun Nov 9 22:26:57 2014 +0300

    PyBoxLib: Fix BOXLIB_HOME for hashdist.

Src/Python/GNUmakefile_CXX.mak

commit 5c85b0b69a4ac1b0feb972b92191090be3ebd4a2
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sun Nov 9 07:10:06 2014 -0800

    PyBoxLib: Tweak BOXLIB_HOME.

Src/Python/GNUmakefile_CXX.mak

commit 0d74e06100607d1a95bf59e2c05d9464cf622fed
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sun Nov 9 05:15:30 2014 -0800

    PyBoxLib: Get 'python setup.py develop' working.

Src/Python/setup.py

commit 01e9a09ff4061b881b4ad2485b761190caf70d54
Author: vince <vebeckner@lbl.gov>
Date:   Fri Nov 7 16:35:22 2014 -0800

    typo, removed old code.

Src/C_BaseLib/Profiler.cpp

commit 8926a71546506fd5eaffea80c3e15f99922132f4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6a51721ecc5e87fb7fff61e1be1a6aa4f5ad8c53
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 7 08:16:14 2014 -0800

    fixed OMP in Jacobi smoother

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit e99db1b1dd033612695fed7cf5b5682ec2532eb8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fd2517a2eb4b9e68594acf654de5275dc5033728
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f1440cc1cf4db3d4d464d183f60dda62ac89b304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 355e8c1b26645dceb0d8854de381c15996cbcd33
Author: ajnonaka <AJNonaka@lbl.gov>
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 4ca1d1bb372d23fa9d443fcc442a329674210277
Author: ajnonaka <AJNonaka@lbl.gov>
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 e0496f13d82c7aaf1c2af36765f5b45d17c90acf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a7f1abb1ab3a82c3eeddac1a545b3b6063b460f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0caf98360757264dd410dc66e1c67d112dc73fe1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Nov 5 09:21:37 2014 -0800

    cims.nyu.edu

Tools/C_mk/Make.defs

commit 42f99fa3a25919714b5bf09bddf9aff2c7684212
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 4 20:14:35 2014 -0800

    make Cray compiler on edison happy

Src/F_BaseLib/layout.f90

commit f2f03607cda3afbfe8199c3a5b6698dc090a4055
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 4 11:32:08 2014 -0800

    wrap up ml layout strategy stuff

Src/F_BaseLib/ml_layout.f90

commit 430d6bb01c4651727b580c1198f024d5da6afa79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 3 16:38:37 2014 -0800

    more work on multi-level strategy 2

Src/F_BaseLib/ml_layout.f90

commit 78367be969709730a20608883809473e73e33f01
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 43592ce07ccc9570d1ba27b7c63af39a48c77e72
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 3 14:08:41 2014 -0800

    Donev updates

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit 718e48b490d6ca683095be60d7ac63ac1098f5c1
Merge: 212d87d f5a5673
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sat Nov 1 19:39:46 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 4e775e2b0a1259621ca9275f4a91b9964d0e2929
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:46:03 2014 -0700

    added comments

Src/F_BaseLib/create_umac_grown.f90

commit d5d2ef0ac4fe4337b85b9d0534e7f11c9ef011b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:30:26 2014 -0700

    fixed the fix

Src/F_BaseLib/create_umac_grown.f90

commit fb6542a83f77ba3752bd6482548471eff65ffed9
Merge: c8f5704 401e425
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 31 14:21:51 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c8f5704dd110cb6037e5d546189a38117cba6793
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 401e425204df077e05577dcaf989cb1190cb759a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 31 14:20:38 2014 -0700

    Add InitCosmo1ppcMultiLevel for IAG folks.

Src/C_AMRLib/Particles.H

commit 2ef059e4ef88e6b15cd500a7c7f4e8d27a7d7a71
Merge: ccbeba2 3ac16c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 17:35:27 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ccbeba2763280eeabc1da7045885c24e8f02fefc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 191392a779fcd3203012e3c4e22fa33016722801
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 58e0846831fc718e4948d09597617c307f841549
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 16:29:03 2014 -0700

    cleanup

Src/F_BaseLib/create_umac_grown.f90

commit e20e3cc66b1011512efa2f1dff28100663bea892
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b5d2c2e59200781a73939a7fd417898cee43ad5e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a0e5536198fdb37db54bc7fdbc320fadef11751f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 30 09:55:42 2014 -0700

    simplify the boxarray in ghstassoc

Src/F_BaseLib/layout.f90

commit 344102889238d3b1511ed56cf3a072d788d9b72b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3aa8cc705072fdfc6e81bc02c805905b19e4c3d0
Author: vince <vebeckner@lbl.gov>
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 8bd20ee9a05a0a13c2117c498585e2a304f04fe2
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 13:49:57 2014 -0700

    optional barrier in ccd.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 8e1355728d22b5dd8774989ac06f83a5a6a542ba
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 12:51:23 2014 -0700

    clean up directory creation.

Src/C_AMRLib/Amr.cpp

commit 39f41edf4ab24eb2209d903c55e3072916dcc4e5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 de72a561b652f3c32339225e2479091d061d7a97
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 29 11:49:41 2014 -0700

    create clean directory function.

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 9aa54a9fd4bf806099e7944c6b629e287a11d7cf
Merge: 5f498f2 3ac16c1
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 29 10:56:57 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3ac16c1be959275b9944b57e483f009155fcd81d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 28 20:34:29 2014 -0700

    removed some includes

Tutorials/HelloWorld_C/GNUmakefile

commit 9cbc3b532e29c8e3672a4dfb158f78616d133435
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 212d87dbea1c78587f6bb6461ae3b368cdb0c647
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 28 20:21:51 2014 -0400

    add a trim()

fvarnames.f90

commit f5a5673f9b9c67756b1178e6e6297fb7c8995014
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 e22594e6282a7dc18df43d24956a291417fc3126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7c96ed74a706076b387980af1742ebaf7edc9475
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc18fd45264e8191ef3579d6c80b64d687da62de
Author: vince <vebeckner@lbl.gov>
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 ad4adf39dd5bd5117dac534000e153ac9f619197
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 15:17:18 2014 -0700

    F90: fine tune ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit 74a7030ef6a1861729245fe4f9b863f5af27a4ae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 14:59:56 2014 -0700

    F90: fine tune ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit 05848977ba471603c42d59c57c21c6bf6dfd7c40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 27 14:20:28 2014 -0700

    F90: implemented ml layout strategy 2

Src/F_BaseLib/ml_layout.f90

commit d35628e8db357c92a67f9d26677da8b488cef33e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:36:48 2014 -0700

    cleanup

Tutorials/HeatEquation_EX7_F/GNUmakefile

commit 32d8f8990c5a7727931c05786d9bfebe0112a915
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:29:15 2014 -0700

    update comments

Src/F_BaseLib/ml_layout.f90

commit 468c8d3179cb6e246e407e4d9e5dba38364b2622
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:27:56 2014 -0700

    F90: use the simple version for tutorial

Tutorials/HeatEquation_EX5_F/main.f90

commit dbb5bfefd7c1e52b4ead08d358a8269b0d1f4057
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 21:20:25 2014 -0700

    minor

Tutorials/AMR_Adv_Diff_F/main.f90

commit b144f3c9e293570a0d575db2bbc6d8d34aca0a73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 246f58f816573dbfb5c01476f2053e049f81b86a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Oct 26 19:38:01 2014 -0700

    F90: destroy unused layouts

Src/F_BaseLib/ml_layout.f90

commit 99b42169f6799c5613794a8b09891ff6abe018e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f2518b854ed6a6ceb18fa6dc3641da626ea159f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3b3bdc9a33ee60991aca4faf07fb927b9bc6fe32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cdf9536cec640385288c2579dbc85b1f4e5d49e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b27c8c89f3fa25ea8b59473d22c1726802978905
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 681acfa47bcb9cd990546ae27b988af831dfff4f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 94b5e30e1eca2773b93c14f04d5a154c87883abf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aa4aac6c2ee0c8f8041a557d9184983085b9d188
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2d864feca536b34eff12def8293131781c07a3e9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b2880812202e98af0316c65c24df8270439c91af
Merge: b0acfa3 43a3e59
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 b0acfa32145eaaed3db3ab66e025ad745d0ba47f
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 43a3e596715cce01e466509b1b1fa726efe74163
Merge: d0d4670 ac1a42f
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Oct 22 18:35:45 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit d0d4670bed07456a058564af2c62184814974c1c
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 5f498f21714cdd5937e032864229aa948dda7260
Merge: 097732a 4a77764
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 097732a57b711a2f5100fcfbee20a0cd4f50035a
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 4a77764da9551f9f1083e719d5fba3c1968c4c68
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 21 12:48:25 2014 -0700

    MLSDCAmr: Use AmrLevel constructors for MLSDCAmrLevel.

Src/C_AMRLib/MLSDCAmr.H

commit 5b9ae5b834ac3ad396723fb1e63b9d971f340f25
Author: Matthew Emmett <mwemmett@lbl.gov>
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 ac4ebc869b6fd98737577decc08f04db43a02dee
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 21 11:16:01 2014 -0700

    added file

Src/C_BaseLib/BLProfiler_F.f

commit 450ae061c7a735f68310296374478552a093cf0e
Author: vince <vebeckner@lbl.gov>
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 56220a15ace9e2d30bbd41f15b42a038c379cef5
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 20 13:37:54 2014 -0700

    added step regions.

Src/C_AMRLib/Amr.cpp

commit 527e14ce603ef6df827e6d8a10d3dd26d37ee5a5
Merge: ccb37c7 873eecb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 20 10:16:50 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ccb37c7bcfbd298b3ac7ee4c98e354a55ceb51a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 873eecb2b4807986605f168e8b1f3339130bcfe2
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 74654043796cd5dcc5f6727ee0ed5bb16e78f223
Merge: bcf8216 a24ba7c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 06:20:16 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bcf8216dc96dff441498dfa1d45976170780adbb
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 9b51ae9bdc1bf1435f09d38d71b3932d37897e57
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Sun Oct 19 06:19:25 2014 -0700

    kraken no longer exists (RIP...)

Tools/F_mk/GMakeMPI.mak

commit a24ba7cbd7af49ddd19dbf0b22c5173b07db8444
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dad3d8db790a330b80244a048c06d2cb11347bce
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 21:02:16 2014 -0700

    F90: added OMP to sfc

Src/F_BaseLib/sort_i.f90

commit d7ed284f178170c445e4d74dcaa63b83bcf73234
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 426264e6bc35c32c75b7c4925f91701de775fbc1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0078faa4093843d9ea7d50ce529bf0acd1434d59
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 17 15:56:58 2014 -0700

    F90: added OMP to multifab copy

Src/F_BaseLib/multifab_f.f90

commit 348f937bb7a02c4b4968ad03292851c480339c5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 58a462d044ffc1a7bd7eaeae6e2b363f706edd85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7ba597eabdcaa8ed46bcb2ee7afc343c1b37d774
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 56497fdda734598cecccec8859e24f7ffa4d1e99
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0da297992b94b3e79ed429e4fdbce5f202766ed2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 75f09a2a707a896f3fa4159c5e5d135b26d2fe47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4ab85659e55dac0894a31c5d40e9f31d33d82dcf
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 16 11:55:18 2014 -0700

    macros from the commprof branch.

Src/C_BaseLib/Profiler.H

commit 467d154897e39de70432c0ba0b47d3b915f59f97
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 2e45c68e62f891b29399de8f9b030a15c91ef748
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc166f9f83abb0331b8fb3d85020e0aa3d735891
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 48041f250573aec4006791e3d475178b34d99c16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4ce509e16c3177abc05da7fbfd4a3bd00dc024a0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 20:33:14 2014 -0700

    clean up the new ml_layout_build_la

Src/F_BaseLib/ml_layout.f90

commit a9e464ee0049db3a6749d941822eef12a3c6b444
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 17:41:23 2014 -0700

    new ml_layout_build that copies another layout

Src/F_BaseLib/ml_layout.f90

commit 40d8a9e0e48945791fcd6072bd1c85d1c31ca209
Author: vince <vebeckner@lbl.gov>
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 b4231c8fdfbec9ca383d3506b53bbb1b549da195
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 78a7012a4022f4b7768a9403680821394c80b1e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d9814bc0208927099dc6bf9d0fc6aef630da12d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 15:20:13 2014 -0700

    F90: removed an unused function that was recently added

Src/F_BaseLib/fab.f90

commit 5c57292054107fe256814ff0b52504ee08056808
Merge: 32b4d4e 837cbfa
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 14 11:11:17 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 32b4d4ea793a08f8dfbb2445478f94f9eadc399b
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Oct 14 11:09:46 2014 -0700

    Add GetParticles method to ParticleContainer.

Src/C_AMRLib/Particles.H

commit 837cbfa788bdb624300ab3234b5313d48b26946b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 14 13:59:12 2014 -0400

    add a description provided by Weiqun`

Src/F_BaseLib/cluster_f.f90

commit 46a935a53676806dfe7d9eaf9653d7a2310c4b46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 14 10:18:31 2014 -0700

    F90: check allocation status of imask

Src/F_BaseLib/cluster_f.f90

commit ccff20077bbe396521ab94d12454b15a3e7e6dc2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 13 17:15:30 2014 -0700

    fixed comments

Src/LinearSolvers/F_MG/ml_solve.f90

commit 902c00908a2581b196d2132066e307d056df89d2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eb39752be20c12aed19347903fd3256f5074734a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8002bb34b2e1b19b03855bcb7ab4f7b1b403eda2
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 13 12:21:44 2014 -0700

    added several regions.

Src/C_AMRLib/Amr.cpp

commit aff2b6470eeacd7b9765e4633dfdaae7d3fed0e4
Author: vince <vebeckner@lbl.gov>
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 178b5087c974d7c2fb826dc2745c0c947b160476
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 13 12:12:03 2014 -0700

    added TRACE_PROFILE and new prof suffix and defs.

Tools/C_mk/Make.defs

commit 1a2c6206a52efbae2edf495c9ef6bfb64a09129f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e649d09c3176b6ba7acfbc9b478e38999ff2cdde
Author: vince <vebeckner@lbl.gov>
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 07cf5390b436e1398539ddf57bd5688c794998c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 16:02:27 2014 -0700

    fixed indentation

Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90

commit 5975e08a51f7dfa68b2183278ed5b080ceb51844
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Oct 10 12:11:24 2014 -0700

    added timer to create_nodal_mask

Src/LinearSolvers/F_MG/nodal_mask.f90

commit c5eb8536637e2bac9688f9dbe5d565f9939b9594
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4cc2d180ee91629b2e04d68d82ae8853e45b434d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 10 13:34:46 2014 -0400

    fix the summary table for when we make benchmarks

Tools/RegressionTesting/testnew.py

commit 9f227718cf00ef9d5db1bd6d5b27c0f0e3f61958
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Oct 10 12:19:55 2014 -0400

    add the wall time to the summary table

Tools/RegressionTesting/testnew.py

commit 9eb66593b3f0c1b5661d9ae159de67ebc9c4f458
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a5a9639792faf333f05e1b8b4ffd33926ac8d3de
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 9 16:46:38 2014 -0700

    added const.

Src/Extern/amrdata/AmrData.H

commit 9f835f6c2b35cb0c8cb0a92178fcd752f3394945
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 9 16:36:37 2014 -0700

    added const.

Src/Extern/amrdata/AmrData.H

commit 9cf518ef043de6b9e29e9971b50538bdb96223c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 16:32:13 2014 -0700

    F90: incresed maximum # of copyassocs from 25 to 50

Src/F_BaseLib/layout.f90

commit 8ac8dc220c09cbed78f1f0ba0ac395db3e37b94b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 9 14:55:53 2014 -0700

    F90: rebuild fine layout too when not properly nested

Src/F_BaseLib/regrid.f90

commit e60032f9cdcb5fd84e82df160dcb22a795bb6de4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bee49d4233edf79edc9bc510c81c967cbc96e6a7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Oct 9 16:45:37 2014 -0400

    prettification

Tools/RegressionTesting/testnew.py

commit 084af4f37ac76237f98949e26535079c51571f2d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 22:28:57 2014 -0400

    make the test run summary more informative

Tools/RegressionTesting/testnew.py

commit c266768acb97f5e68885b52361e0a312c4ae8786
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e8e713ccaea15a5c4854523cff24e613a85ef580
Merge: 7a906c5 7778afd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:38:31 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7a906c517bd7d75feb27e5ca0a784b07e0517b2e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:38:14 2014 -0400

    latest version

Tools/RegressionTesting/Maestro-tests.ini

commit ac1a42fb8a693eafbe34a7efd47d0da62c4e1591
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Oct 8 20:25:22 2014 -0400

    fix compilation

fboxinfo.f90

commit 4ed45302b4dbbabbbbde0a6c412b0be6eae85b51
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7778afd142f92eb74c4cae8245cb9f3a5239b502
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 16:34:43 2014 -0700

    F90: ignore fine in layout mapping

Src/F_BaseLib/regrid.f90

commit d753111f589bab69c46dc12d2a285f1f89345f22
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e6d24ecb51ad6093eb875ae491e8fe65c8ac3a9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 13:32:03 2014 -0700

    tidy

Src/F_BaseLib/regrid.f90

commit dfd7e0d2018744d83e188a4c1b93ea04ce94ffd8
Author: vince <vebeckner@lbl.gov>
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 5f913d5d04be7d135d4c2172a2c615b8d3e7f935
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc636e228d0838c43f416e9aa11e7305e0d66992
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 8 10:21:57 2014 -0700

    moved text call tree to postprocessing.

Src/C_BaseLib/Profiler.cpp

commit 0f2ce161f34bb284be1e9c9b1ba94c5e796e9ebb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 8 09:49:58 2014 -0700

    fixed a bug in miniapp

MiniApps/AMR_Adv_Diff_F90/compute_flux.f90

commit aeb271c3851387d733e88ce1b87b1f988a61557d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 58a0e4b62322ba4d2c0b0fc881341b2eb5bf444e
Author: vince <vebeckner@lbl.gov>
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 67a871c36851e7c239f4159220e3bc83fb04d17b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 79067bf3d654248f7e035e8284513623f9b35376
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a21e8ec738742c452a35ee0a4cf861e8740d3186
Merge: 1bfaa27 b7f6467
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Tue Oct 7 14:01:49 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1bfaa270dba589841a364fc080d491454933c56c
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 b7f6467cb975f2353b67ea0c6f3a8eece03e8304
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a6ebfbe4c025a0e9f4601cc4570159bebfdcbd97
Author: Ann Almgren <asalmgren@lbl.gov>
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 5066221ea0a44ccfa621b2928c4bd6b93eb9e219
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e28b9d87f103d4290c85551e09566a72e64587b8
Author: vince <vebeckner@lbl.gov>
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 a1641dbe8c0a14c8174509480578382df5afd552
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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_EX4_F/regrid.f90
Tutorials/HeatEquation_EX5_F/GPackage.mak
Tutorials/HeatEquation_EX5_F/regrid.f90

commit a00688229ca4454c972fbc9cb58edb9103c59ef8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ca7dd1be5ea9abc5835abc411b1f53ccf05be600
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 6 14:57:19 2014 -0700

    added a new line in printf

Src/C_AMRLib/Amr.cpp

commit 370b48f2499a7a75c237c0353c06333d4174e070
Author: vince <vebeckner@lbl.gov>
Date:   Mon Oct 6 14:10:51 2014 -0700

    fix for serial.

Src/C_BaseLib/Utility.cpp

commit 4dd0bad1bdf77375393824c48525144775291bf1
Author: Ann Almgren <asalmgren@lbl.gov>
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 baf8b89b9f49cf0de64c7f986046f10f8cf81e45
Author: Ann Almgren <asalmgren@lbl.gov>
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 7f3d4bbeac88087b04d66d8b95e47740e04c6f92
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 12:59:20 2014 -0700

    Remove unused variable.

Src/F_BaseLib/fabio_c.c

commit 64423961a2e46d6af43465e2ecad6fd0c261d996
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 6 12:47:40 2014 -0700

    Remove unused variable.

Src/F_BaseLib/layout.f90

commit 9ba4c92e1f2cba33886151aaf23e3bbd8926ebdd
Author: Ann Almgren <asalmgren@lbl.gov>
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 c746d720e8929abba03428237a9fb0a10aaf3026
Author: vince <vebeckner@lbl.gov>
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 2c46931bb538475c84defef18cb6b876934ecd16
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 2 11:10:40 2014 -0700

    mask for NoRegion region.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 75bd8e606dfc9955559b26381c9fd3a7825a6e2b
Author: vince <vebeckner@lbl.gov>
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 7dfe73e403ff741eb506f03faa4af5ce095afede
Author: vince <vebeckner@lbl.gov>
Date:   Mon Sep 29 16:07:18 2014 -0700

    streamlined binary callstats format.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit af04e63e716a8b2716f57f95d96f2d38d8e156c9
Author: Ann Almgren <asalmgren@lbl.gov>
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 f55f4cc18b99b68d00beb2aa8272bdaf3f57f116
Author: vince <vebeckner@lbl.gov>
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 e5f96414a1828d61412c66a34bef3d6b27266d7c
Author: Marc Day <MSDay@lbl.gov>
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 d86dca967149a35699b2964a53b58ce887ffc450
Author: Marc Day <MSDay@lbl.gov>
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 25009c95a3ead625599a882d3030e05cb5c34b9b
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Sep 24 11:26:11 2014 -0700

    PyBoxLib: Add --disable-mpi build option.

Src/Python/README
Src/Python/setup.py

commit 6023c0f415d58d6946e73a38e0b1292527a9ffc8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 583ed864bcd8d6275c73d3826eebe3d2f8327082
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 23 13:14:37 2014 -0700

    PyBoxLib: Honor USE_MPI environment variable.

Src/Python/setup.py

commit 747677fbec6e1eb31f35a3912aa0d41f8998a301
Author: Matthew Emmett <memmett@gmail.com>
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 ea8f0722c55e3ad7e32f1de840f3b77fbc4bd01c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 16:51:52 2014 -0700

    cleanup

Src/F_BaseLib/ml_layout.f90

commit 3428935558f000090ead59ca9c7f7528f8440f79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 144f74de9a8c28992897fe4c33acb3b0868bdcbd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 15:16:46 2014 -0700

    clean up

Src/F_BaseLib/multifab_f.f90

commit 7aa7f9ae38eecfa4a53322c366f22c1ab25c46ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 22 14:49:39 2014 -0700

    removed pingpong.f90 from CMake

Src/F_BaseLib/CMakeLists.txt

commit 5700ab0d43c97dd5bde441e057fde4151af8e06a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bc682fe123cb1685cb2d101aa7746d38531c2774
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0fa8fecb012662e9f19edb5e2639cb2371c9f9ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1779e3212b9e77333c0b5b7fb23fc4cebeef5fb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 96b1c7e355e8af4f7a78079e9975791953a2958f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 19 13:59:10 2014 -0700

    added nooutput option.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 224e8f29e2db27c298332b164bb7c7c0698ca3c9
Author: vince <vebeckner@lbl.gov>
Date:   Thu Sep 18 11:56:21 2014 -0700

    more region profiling.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 17134e99b6bf54875ed6184c88f228cb6fb128a1
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 16 14:36:12 2014 -0700

    Uptick version number

Tools/CMake/BoxLib_Version.cmake

commit 72af319e46b4a358b3f025e032c5aac3dcc251b4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 16 11:26:04 2014 -0700

    minor cleanup

Src/F_BaseLib/layout.f90

commit 62faf77edc2e11156bc8a237abc45ba94f838179
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Sep 15 22:13:16 2014 -0700

    PyBoxLib: Fix inclusion of libgfortran and libquadmath.

Src/Python/GNUmakefile_CXX.mak

commit 6d76522c5692d16fab1a9dd462a1ee604ef89ef6
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 15 10:52:54 2014 -0700

    PyBoxLib: Add library path for quadmath.

Src/Python/GNUmakefile_CXX.mak

commit 41f294e6c730271effffbba8fa451a2a5f3314c8
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 15 10:52:32 2014 -0700

    Make.defs: Increase template depth to support clang (LLVM).

Tools/C_mk/Make.defs

commit 300e7d0147d7e36a17e1d2e042e1e5891cf1a8ac
Author: Matthew Emmett <mwemmett@lbl.gov>
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 411d14b84997987225380a1ac3f45fe695263663
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 15:30:06 2014 -0700

    PyBoxLib: Simplify PYLIBS.

Src/Python/GNUmakefile_CXX.mak

commit 3aac5cbbb60de1576d110fa3a7e0ae3bff2d0a76
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 13:15:33 2014 -0700

    PyBoxLib: More trickery for Darwin.

Src/Python/GNUmakefile_CXX.mak
Src/Python/setup.py

commit 9aa9d65f0b29c2c5116d9ccaf3ed5f23e272d8bf
Author: Matthew Emmett <mwemmett@lbl.gov>
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 6f07ac5fe387103dd7c7779fc6483cb2ca8e28e3
Merge: 2ab9a79 d0d1804
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Fri Sep 12 12:15:48 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2ab9a79e6a2845d8921236aeb0e067a23240ba28
Author: Matthew Emmett <mwemmett@lbl.gov>
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 b007d08249c2ff15a901f25dfd935b00f2135b20
Author: Matthew Emmett <mwemmett@lbl.gov>
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 d0d1804a5fcd8245e0238ee63027e34e6f61022f
Merge: bde18b4 a05e9c7
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Fri Sep 12 12:39:07 2014 -0600

    merge
    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bde18b4598120ca93ee1f4beb085b8c1f63f808b
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Fri Sep 12 12:39:02 2014 -0600

    dont use libmpi_f77 on my Mac!

Tools/C_mk/Make.mpi

commit 35a84299208640e55c64f2612df57ded7c7024c6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:34:15 2014 -0400

    change option name

fcompare.f90

commit 7bb7f71fe00044fc50337e1211ce5800bc8d68e5
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:20:19 2014 -0400

    start of support for outputting a plotfile of diffs

fcompare.f90

commit d6190aa6cb30f6ed9a6dcc160a16705ca2027870
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Fri Sep 12 14:17:37 2014 -0400

    layout_build_ba now requires the pd argument

tutorial/fwrite2d.f90

commit a05e9c7ab0fa569e9a861c1ff24ee4081b1ebc79
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6329719097c61d27455a03c74ed541530dd20a7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 22:09:13 2014 -0700

    minor update in F90 flux register

Src/F_BaseLib/bndry_reg.f90

commit 88c485fe1969cf2ee99978ccc9bf1bf296b94ca1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 07c19734ae0d68db2bf220d7d200b8acbdb60734
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 9 10:59:33 2014 -0700

    remove some outdated comments

Src/F_BaseLib/multifab_f.f90

commit 6d1769712fc62d3acd39bdbd6f62f21fa248e74e
Author: ajnonaka <AJNonaka@lbl.gov>
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 16f7db573430367f004cafafbefe97940915357b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 57fc4432a6a678c0c146e78321390c1dba5fae5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4d3235ef8c969d0234903ac5ae7cc344445a515d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b17a5e6e39b69d1ff61150280071423956ceb8d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 8 13:41:23 2014 -0700

    forgot to add in last commit

Src/F_BaseLib/ml_restrict_fill.f90

commit e26bbe732c785c0f1f829c64e6c5242bee183a08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 302c356d44a93415e9b42249e88f6bf4004d9f27
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 40a9a340a27a64a96f72c83220f8a7319fc40387
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ba6747797ffae82acdf5348646730431b80ea96
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 17:32:34 2014 -0700

    added a stable merge sort method

Src/F_BaseLib/sort_i.f90

commit 4acef2d6f0bbe2a4b9ac5ab410d5b05def57ec47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9f96db6311c2c5325593c49c951c1a520d429edb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fc84b779e994f4395ac18b6a04c423d0f64ec63e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9fae6ff55fbf8174813062fcbbb426f344dec62a
Author: vince <vebeckner@lbl.gov>
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 5ddc6bf51294ba416d1c607570558fa38c4c8760
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3826da2fd31cb57eb78199f0ddeab30978c60698
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5b0fcce7be4f6b447a237f151039ea7de0e1c392
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 5 08:24:55 2014 -0700

    added flux register for subcycling to F90 BoxLib

Src/F_BaseLib/bndry_reg.f90

commit b7c6912e2a6709203af2e65ffe49dd71878c7802
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cfb267b14706d95a887dc569db3192422a3fcbf4
Author: vince <vebeckner@lbl.gov>
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 f9d787e4a7ef4acdbcce6a2c90c5076fc8ad2158
Merge: ab8a680 065c750
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 4 13:23:25 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ab8a6808af5ef835a293f0a341567704b01ee9ee
Author: Ann Almgren <asalmgren@lbl.gov>
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 065c75096301a2e8532ae68fce1fda2c898bdac0
Merge: 37dab02 3d53b47
Author: Chris Malone <chris.m.malone@gmail.com>
Date:   Thu Sep 4 13:51:06 2014 -0600

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 37dab025e854417b5dc738f984e6dd5ba83a8c7d
Author: Chris Malone <chris.m.malone@gmail.com>
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 3d53b47c47e1beffba50f77b4c98cda8293b4940
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 7d0da310d7e3b344c5169a70dac0c77fdb6a0ddf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7db79010ca73fbdcff4acaf42cb9b73dc9a606d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2a823fe17d7f29fae69815aba4b10e8a3a025329
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 3 17:54:34 2014 -0700

    intent(inout) --> intent(in)

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit 252e00b00abf0212aeffc2af6b41ba428e7735f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 96da97b5c786865122e2a5e3d8e7bd6d59a217ff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0235a7cb572defa3da96d61fe4de9807c02dc921
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 398b40a118051869d8d014e0469f09d3bee02a24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 de54f06628e4c991f20cd13e081c2e8366f5c7eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e3947dff4aecd91401229b6fc880f15571d36c58
Merge: 9eaa4fb 5a30282
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 29 10:42:17 2014 -0700

    conflict fix.

commit 9eaa4fbfb74bc0181cb1edb151508ce9a4ac8f4d
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 29 10:36:52 2014 -0700

    added profiling.

Tutorials/MultiGrid_C/main.cpp

commit d01e5bc06e4ab2056538ecbcfb74acd34ee5fb26
Author: vince <vebeckner@lbl.gov>
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 5a30282cc2b353eee71168f9cc53e5cbd98a47c2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 28 20:30:13 2014 -0700

    updated fillpatch_t too

Src/F_BaseLib/fillpatch.f90

commit c018de6d306ffcf9e05fc07832250dc932263bdb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6a45fbd5e64640c3019eb089350331cb4352d6a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a2c36dea7d908d90c00982bbceefd1ba9ba9289e
Merge: 2aaecc6 d5d6d13
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 28 18:12:10 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2aaecc6daa1d2e44aa3b71a30f8e88bcf9a82172
Author: vince <vebeckner@lbl.gov>
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 d5d6d13818869d8dfe110d4a3a14a74ef53ef964
Author: Chris Malone <cmalone@lanl.gov>
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 6b9e8ce762c718bf84071d0b1569b43af9c24383
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:55:43 2014 -0600

    remove vestigial loop

Src/C_AMRLib/Amr.cpp

commit d782c727f35810dffc923f60ee395e3205c147ae
Merge: 9ab74b2 cc235eb
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:53:53 2014 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9ab74b206de993432fe84c5b31a0a01451340dfe
Author: Chris Malone <cmalone@lanl.gov>
Date:   Thu Aug 28 10:53:38 2014 -0600

    updates for LANL machines

Tools/C_mk/Make.mpi

commit cc235eb7ecf20e95f86fc7e8ab4e383c96470c53
Author: Ann Almgren <asalmgren@lbl.gov>
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 430ebd8bd5a397788fd7527af3028a71c28893cf
Author: Ann Almgren <asalmgren@lbl.gov>
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 2df91d9f562afaa1389c8f85acfcfd8c3a127cf1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 20:29:53 2014 -0700

    This is replaced by README_F

Tutorials/README_HeatEquation_F

commit 7dc3b5fb06f0b67d3686e94ab5cfcfe7ba0d68c2
Author: Ann Almgren <asalmgren@lbl.gov>
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 bc17c64390ac7115d933e303a5a607a9f9a1e489
Author: Ann Almgren <asalmgren@lbl.gov>
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 d018d1381eca70dc2419dceee31b1cb9f68fe398
Author: Ann Almgren <asalmgren@lbl.gov>
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 e795e57708fb1808e47abac272cc23f706abfd69
Author: Ann Almgren <asalmgren@lbl.gov>
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/bc_functions.f90
Src/LinearSolvers/F_MG/cc_applyop.f90
Src/LinearSolvers/F_MG/cc_ml_resid.f90
Src/LinearSolvers/F_MG/cc_restriction.f90
Src/LinearSolvers/F_MG/edge_restriction.f90
Src/LinearSolvers/F_MG/ml_cc.f90
Src/LinearSolvers/F_MG/ml_nd.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_divu.f90
Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90
Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 58d9bc58925d6facedfbfdc6650390810e1822d1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 27 18:00:47 2014 -0700

    Dont have regression test in the miniap.

MiniApps/AMR_Adv_Diff_F90/inputs-rt

commit e176ed36c160904eea1c14cbf8de2525317eaf13
Author: Ann Almgren <asalmgren@lbl.gov>
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 a36e8d2df48a2931fb5cab8e502eedd89325e06c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3d0f4275855759aa34f38520bb7518294641d3b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 15:49:18 2014 -0700

    added timer to boxarray_boxarray_contains function

Src/F_BaseLib/boxarray_f.f90

commit 0a6774dc22acf13c84700c915d51ebe2c2292516
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 27 15:33:48 2014 -0700

    output cleanup.

Src/C_AMRLib/StateData.cpp

commit 1fbfb53d77fdcad99180d787fa79168d2823e302
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 27 14:58:29 2014 -0700

    remove redudnant resizes.

Src/C_BaseLib/DistributionMapping.cpp

commit 5e55387bc18ab6540dbc9338e527b85187cd63d8
Author: vince <vebeckner@lbl.gov>
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 24205dc4c54761f0aa676b31b55c8376f270c2c7
Merge: 2cbacf8 3dfcdd2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Aug 27 10:26:41 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2cbacf88d11e2b2a6d7bc719dfa3458954e6de8a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3dfcdd21b020a0fa5bbffb5cdf6a8d61b989d1a3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 26 16:41:51 2014 -0700

    Fix name of MultiFabTests to be consistent with others...

Tutorials/MultiFabTests/GNUmakefile
Tutorials/MultiFabTests/Make.package
Tutorials/MultiFabTests/MultiFabReadWrite.cpp
Tutorials/MultiFabTests_C/GNUmakefile
Tutorials/MultiFabTests_C/Make.package
Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp

commit 1a21508d2abd8530088cad6efd619e83624b5693
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 26 16:36:27 2014 -0700

    Fixed comment re particles leaving the domain.

Src/C_AMRLib/Particles.H

commit 21a7406fb9bf141a176821fb12b1001f46c2cf7b
Author: Ann Almgren <asalmgren@lbl.gov>
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 aaa16e9b262281da56484c9f745188ee4c38ceeb
Author: vince <vebeckner@lbl.gov>
Date:   Mon Aug 25 17:24:53 2014 -0700

    more diagnostics.

Src/C_BaseLib/DistributionMapping.cpp

commit c54fd284d0bc2a4987c1d9f97a3a354a45552eaa
Author: Ann Almgren <asalmgren@lbl.gov>
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 1701f4e1bf1c93ff449462ac3480505f87adee04
Author: Ann Almgren <asalmgren@lbl.gov>
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/CNSEquations.tex
Tutorials/Exp_CNS_NoSpec/GNUmakefile
Tutorials/Exp_CNS_NoSpec/GPackage.mak
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
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.h
Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.x86.c
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
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/Make.package
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
Tutorials/Exp_CNS_NoSpec/HyptermKernels/README
Tutorials/Exp_CNS_NoSpec/README
Tutorials/Exp_CNS_NoSpec/advance.f90
Tutorials/Exp_CNS_NoSpec/init_data.f90
Tutorials/Exp_CNS_NoSpec/inputs.jbb
Tutorials/Exp_CNS_NoSpec/inputs_3d
Tutorials/Exp_CNS_NoSpec/main.f90
Tutorials/Exp_CNS_NoSpec/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 8ee1a9a99c3c78f899a11b9211aa895993be1cd5
Author: Ann Almgren <asalmgren@lbl.gov>
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 6e7b42c742ae52e3b571374ceb8319e2302709b4
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 22 12:26:23 2014 -0700

    nstates.

Src/C_BaseLib/DistributionMapping.cpp

commit 11f1aa1a2d7a4663c802e1c926d35195cda1930e
Author: Ann Almgren <asalmgren@lbl.gov>
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 afd2e1e74668ba9f41f9371a0892ad99fe039c24
Author: vince <vebeckner@lbl.gov>
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 ad3e5b8cd78e73e006525d0d55d6164a7490fee2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4df26c59d4545be58573410010824a082eacb203.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt

commit 4df26c59d4545be58573410010824a082eacb203
Author: Ann Almgren <asalmgren@lbl.gov>
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 1f1b4a4cd2a05fe809a51f7905fb0e4d994b6885
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 014180e0931b862f17422e0ff4241bfe2bea9d0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f25650574df7aaeb189b4dd56b1ed5774ba7b55
Merge: f6d15d3 b631255
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 14 22:12:58 2014 -0700

    Merge branch 'master' into dev

commit f6d15d3e10b76af2800c7206980afbaf2739a6f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b631255b010e038d9a9a792059a317187441f13b
Merge: 9ccbaff 7f2ede7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 14 12:34:08 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9ccbaff9d812bc4ee6050ea854775c3b65672eec
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 14 12:33:45 2014 -0700

    CIMS machines

Tools/C_mk/Make.defs

commit 7f2ede7bf5995cb030be2da213e05b6d5fff834c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 14 11:24:02 2014 -0700

    Fix the stupid typos from the last commit.

Src/C_AMRLib/Amr.cpp

commit 5596d482b201f2b8491545d0fee21ab1ebc22cad
Author: Ann Almgren <asalmgren@lbl.gov>
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 18ade79e8847f1ec597db32601f03ddcb97d7889
Author: vince <vebeckner@lbl.gov>
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 ea84920cb719b102d98ada3ef883ef832fd63761
Author: Matthew Emmett <memmett@gmail.com>
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 d7261903fcf40a9f6e3bacd91546a16ebc435fef
Author: Ann Almgren <asalmgren@lbl.gov>
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 a93d7777c9ca61bc99353ac57735c3105945232f
Author: Ann Almgren <asalmgren@lbl.gov>
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 20b852d49e5e94ac74d2573237964c3f0bbdef6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 13:41:41 2014 -0700

    Update subcycling description.

Docs/F_AdvancedTopics/F_AdvancedTopics.tex

commit 20542b726256602947deb55fa3ab9e3a3b01edf8
Author: Ann Almgren <asalmgren@lbl.gov>
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 8afaec318b67f5a302fd105b5b4028763809c42f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:10:20 2014 -0700

    Set NDEBUG = t

Tutorials/HeatEquation_EX6_F/GNUmakefile

commit 6055867ea40201743d80535576bba3151db63038
Author: Ann Almgren <asalmgren@lbl.gov>
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 d06098e2700b0608e509d01b10dee30ea6f9553c
Author: Ann Almgren <asalmgren@lbl.gov>
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 4c9f90343aba8090b8e1de46b69663bd5fdf07dc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 12 09:01:36 2014 -0700

    Fix bndry_reg copy when n > 1.

Tutorials/HeatEquation_EX6_F/advance.f90

commit f822518eed014eab7d13b5746b98531ca751d0cf
Author: Ann Almgren <asalmgren@lbl.gov>
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 878a412df36ac9f0b1d80cb4a2f873628f9a4780
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Aug 11 15:57:03 2014 -0700

    PyBoxLib: Add python libs to linking stage.

Src/Python/GNUmakefile_CXX.mak

commit 6dcde9ac13549c7dfd80954281e74aac011a1abd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d0caacb5331fca64ccd1b0cb5da67928d4916d4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 12:16:48 2014 -0700

    fixed typo

Src/LinearSolvers/F_MG/itsol.f90

commit 7caea75c48dc6f18cc148cebb24847279eeec7db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 12:13:31 2014 -0700

    removed more unsafe saxpy; clean up

Src/LinearSolvers/F_MG/itsol.f90

commit e211b62e103f755280573c6b05670bb18eac789d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 53bc43048345a0fe3aad107166622019bd063bb3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aa6db09b8e0c1234f16edafa65ef6cecdf1dade3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 11:19:05 2014 -0700

    fixed a new bug

Src/LinearSolvers/F_MG/cc_ml_resid.f90

commit d9789a27ce22d5637da95f2b55f6917182ef1866
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7a1a2f19643f0be836c4822d083b4216df8af7c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0aa8e642fee01935346ca60af31b52aee5dd464d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 8 09:18:52 2014 -0700

    cleanup

Src/LinearSolvers/F_MG/ml_cc.f90

commit 9f69981543dfd21b7beb8c96cc3e324b40420337
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cc5c0596b380ed88d94eebd78822561f301191cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aad555467e36e1bbda0b8d532f5016c2a7958e8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 21:50:31 2014 -0700

    cleanup

Src/LinearSolvers/F_MG/ml_cc.f90

commit 755904a853a318dc7cdf1fc2db64524426194969
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f216b9e07d1d1546dbc710eba0086d1c087d9455
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 65ea5ac81940031d3cf1db05961522a04ec14248
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 7 14:58:17 2014 -0700

    Modify loops ... still some more to be done ...

Src/F_BaseLib/bndry_reg.f90

commit 779b8cac1feb961b1c8211bf83d1283767f81bff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5dadf95d1d55b19c986515eb055b7c3e23054c8f
Merge: f4ac7b1 ee33126
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 12:48:50 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f4ac7b1b532447560d8b833f8c02928876592c6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ee33126bc005b265d59a75b81adfd0972a762d8e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Aug 7 11:41:42 2014 -0700

    Fix the section on the bndryreg

Docs/GettingStarted/GettingStarted.tex

commit 051007b33d53e6b7f1842130537847c4a33cefb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 7 09:30:04 2014 -0700

    get around Intel compiler issue

Src/F_BaseLib/bndry_reg.f90

commit 90970c877c3275450a6137aa4523d040cf3adfb3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a007d5f472c0938b0bc7128c6772f60bf23610d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 758487bfef80b1437ad6803295a9e7879de5599b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 37a48c0fa7e24d1309dc06ae5a0f4f9f4abd4650
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 905e7e913cd4de26d5731b1ccee2c3eab56c9f6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 97ef6677303dab19a68da19157e282a1c16f7a5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1ab3b18571ca611a214b4f7c0a92708e12a86f19
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 94b1fb9cb27a54f01cc98140f4f065340a568ffd
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 1 08:34:48 2014 -0700

    Add this subcycling figure.

Docs/F_AdvancedTopics/subcycling_algorithm.eps

commit 071c456c3f59051980604ff726fe88baa8a46e50
Author: Ann Almgren <asalmgren@lbl.gov>
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 a8a98c259caf8cf1f4eb9b1b16292111e6682a6c
Author: Ann Almgren <asalmgren@lbl.gov>
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 a8a1f20d7af61c8a681bc41df5562e01a23fae7a
Author: Ann Almgren <asalmgren@lbl.gov>
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 b9007785d1a00cd2faba29b20ac945a8b5b44b3e
Author: Ann Almgren <asalmgren@lbl.gov>
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 b598f581279be99ba07fe81c64c7e42601cbcfac
Merge: 45f3ed7 3e216cf
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 17:40:38 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3e216cf766fdffc0c9246d2450dbd15b2e28f272
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 645f5c302e2f8ab1e922e806a4c95745566e0acb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 32880836c5f94e18eade5ec839278f3119756895
Author: Ann Almgren <asalmgren@lbl.gov>
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 45f3ed75d14fa50a1141434bae3751b983b2089c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jul 31 15:03:30 2014 -0700

    Fix spelling error in comment.

Src/LinearSolvers/F_MG/nodal_stencil_fill.f90

commit 12d853d445a891013525693ef4da62b23cba42fc
Author: Ann Almgren <asalmgren@lbl.gov>
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 e739f60b748475e93591262767dcf0625128fed4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 25 15:32:52 2014 -0700

    added USE_ACC to the make system

Tools/C_mk/Make.Linux

commit 1e91cc83cf37e55789227d5d0836c126a35e5b4e
Author: Ann Almgren <asalmgren@lbl.gov>
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 b24594a438715a7d1194a431766889794456d095
Author: Ann Almgren <asalmgren@lbl.gov>
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 b1bb6b85f119941f8e83aed0a98657f9ba2ee65a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 85ad24c56b118d0b04011f61cfe3a2cb312cbcdf
Merge: ce201b0 c61743c
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jul 24 17:53:58 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ce201b0f6cafb91f1c5a34664bff5cf4a32a583f
Author: Marc Day <MSDay@lbl.gov>
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 c61743c595b4966e2ae03affa27e2b6c86f949c3
Merge: d1d0f7e 453813e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 24 18:26:05 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d1d0f7ef927cee0d8289da280fc9d2e896ec15fd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Thu Jul 24 18:24:23 2014 -0400

    sync this up to file movements

Tools/RegressionTesting/Maestro-tests.ini

commit 453813efb50ddccb8e2a32ebba891f7eb9ff100f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 6feadce488e8b6fc17eff9a515367b08b03236bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 25f5591b7b0bdd8408ad7ff4c5b7451c65587e68
Merge: c072688 25f5094
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 22 16:19:19 2014 -0700

    Merge branch 'master' into commprof

commit 25f50944635873a8bf8755136567619264a1a5c0
Merge: b743379 a25f8b4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 16:11:35 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b7433798b38d5897e08040cc1aae79836b186350
Author: ajnonaka <AJNonaka@lbl.gov>
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 a25f8b4c621874d3b39fa9fc7f6cc97852339838
Author: Ann Almgren <asalmgren@lbl.gov>
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 0f7918cfa6aa4dccf43d604005a443840e0554e0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 22 11:23:55 2014 -0700

    fixed a bpt_build error

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 536d0a0993849a0e4486c8e5bde9f02ed2d70d92
Author: ajnonaka <AJNonaka@lbl.gov>
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 a2ac05590d658fea93fd8da0898b7d9d21a1f7c7
Merge: a3e8320 2bd1908
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Mon Jul 21 18:42:28 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a3e8320e7fb97bce4ba1f078ed9113f35fd4e569
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 2bd19084ac507e42cf4075bdf591f0c4e58a113e
Author: ajnonaka <AJNonaka@lbl.gov>
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 c07268824283b5cae612d2579e3ca7c0d8d104ac
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:37:21 2014 -0700

    added text for fortran90 interface.

Docs/Readme.profiling

commit 3b260c9bf898a29dc2540fe373417ed506bbbb16
Merge: e2354eb 2b5e43b
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:27:45 2014 -0700

    Merge branch 'master' into commprof

commit e2354eb9492852b1df730fe9b10be59455c30229
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 18 10:26:41 2014 -0700

    formatting.

Src/C_BaseLib/Profiler.cpp

commit b52ff318379bfb5dd862c2509d6f7555f4b715fe
Author: vince <vebeckner@lbl.gov>
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 2b5e43bea6b2d529532a9d19aa35b0ccd862fb71
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date:   Wed Jul 16 19:57:55 2014 -0400

    some cleanups

Tools/F_scripts/makebuildinfo.py

commit 0d7c698582fb42a0fafb8fddfad446b14f6b9393
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 0d56865ff24dbc01de9e476efb5a58ed8471a84a
Merge: 1c9f051 3260772
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 15 11:23:03 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1c9f051fa12d36926289c96e257274365085d605
Author: Ann Almgren <asalmgren@lbl.gov>
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 326077234d783477cbb5f3a70edebbc1220c7953
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ed5b71e27b09fe3119cacb0ce5c425378fa1e7ba
Merge: 8a644a4 780853b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 14 11:02:24 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8a644a46fc69df022638101b4e7e7f8ad3a3da9a
Author: Ann Almgren <asalmgren@lbl.gov>
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 780853b46922792246e11496caf3ec8d7300194f
Merge: ddaff3b 6b1edc6
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Jul 14 10:54:20 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ddaff3b70ab406e313d67a3d0c7d2e2d9a0b6ab9
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Jul 14 10:54:03 2014 -0700

    PyBoxLib: Use F90 for linking and include -lstdc++.

Src/Python/GNUmakefile_CXX.mak

commit 6b1edc60982df9743353bea34dedb6b9d298166d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 14 10:47:34 2014 -0700

    replaced -1e200 with -Huge()

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 495029f4eb0b432f9f786647bc695b000d982d40
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 a06f54de5974e00f234498c4747a6612075a4525
Author: Ann Almgren <asalmgren@lbl.gov>
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 3721759e242fa32aa9fb8cc41662b17012b47524
Author: Ann Almgren <asalmgren@lbl.gov>
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 b605b51a0fc1e3a29e52565649f4457afa243b4c
Author: Ann Almgren <asalmgren@lbl.gov>
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 129d55e3e8c22ead41633e2930400c67ea7cb46f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 1e250c69577e29b87e7fabd73d65cf80e081018b
Author: Matthew Emmett <mwemmett@lbl.gov>
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
Src/Python/src/boxlib_wrap_2.cpp
Src/Python/src/boxlib_wrap_3.cpp
Src/Python/swig/boxlib.i

commit bb37bf272b24e80cc74bc96e499be23fab004583
Author: Matthew Emmett <mwemmett@lbl.gov>
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 e1f3d1a07b696526196fc09c216e4256eb4375a4
Merge: 862258d f12f52b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 1 16:44:06 2014 -0700

    Merge branch 'master' into commprof

commit 862258d6d0f0632bd84fcf531d6d2c75d654c900
Merge: e97d9f0 080b972
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 1 16:42:14 2014 -0700

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit e97d9f051b76a58ccad1dd472814b2f4f947d74d
Author: vince <vebeckner@lbl.gov>
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 f12f52bd5c02060bfa819929260794e08f62d893
Merge: 574aee2 9bf14a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 17:37:30 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 574aee2f952fd9bf37eceeb30498f445357aa49f
Author: Ann Almgren <asalmgren@lbl.gov>
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 9bf14a83268a4c08fc9862b115d303fbc0d32041
Merge: ce158f6 5cca58b
Author: Chris Malone <cmalone@lanl.gov>
Date:   Mon Jun 30 16:14:01 2014 -0600

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit ce158f6887173248a79c1a0a3f8b1b272111b365
Author: Chris Malone <cmalone@lanl.gov>
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 5cca58b075795b00909a7a527b31a8edb905d9e6
Author: Marc Day <MSDay@lbl.gov>
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 080b9725bde9113fd5c7a69e3aab729ba166ab81
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 14:32:00 2014 -0700

    Sync this up with the master version.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 5888eccc4654ed495f8d83ae6175a43b3af6c9af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 14:30:34 2014 -0700

    Fix the print statements ... hopefully.

Src/LinearSolvers/F_MG/ml_cc.f90

commit fa4b2ee65ea59c757c9ed37c95ff1ba733c643b1
Author: Ann Almgren <asalmgren@lbl.gov>
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 d13e02184a244ac50144d54df45006b8127165ff
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 30 13:40:07 2014 -0700

    Correct spelling in comment.

Tutorials/HeatEquation_EX1_F/main.f90

commit ce0fbd7501113cb3b6caa30a1f40dfe1c49cd4c8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 8d9b8abcd1dcdf2e7f20229aa06ef3e1f48a825c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c7fc604f4a5c4ac04f0e6f695d5d8d374ef14483
Author: ajnonaka <AJNonaka@lbl.gov>
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 0119511cfa881b101b8731c91777f74a68db860b
Merge: a23398f f3d3842
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 25 06:25:38 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a23398f9c874541d68de5c72a17e789c08be5fe2
Author: ajnonaka <AJNonaka@lbl.gov>
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 f3d38423d0077995254934a69d71cb058be79e9a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 014f1ee6f1e053ae30e022097aaaa96b2d566f31
Merge: 6900956 84f12ef
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 24 17:01:58 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6900956dc7f77f053cb42249822b4b034f23d3cf
Author: ajnonaka <AJNonaka@lbl.gov>
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 84f12efcf49d6e9bbb4306b2d629337b79eb2b2a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 e11164c814cba460ecf3fb8da6f42b642e35382f
Author: vince <vebeckner@lbl.gov>
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 f35f8004ce120fa679b20f141306711e417c55a5
Author: ajnonaka <AJNonaka@lbl.gov>
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 c8b351a588a2cbb72f22b2e1e88e548c4d7200db
Merge: cc4d7fd 842af46
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:19:27 2014 -0700

    merge fix.

commit cc4d7fd8da0e10931b7517388801a3f2a5fa0394
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:13:39 2014 -0700

    bl loc.

MiniApps/FillBoundary/GNUmakefile

commit 401bb2ca183144702e4411fd51504bb4e2645f4c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:05:00 2014 -0700

    more pfc.

Src/C_BaseLib/DistributionMapping.cpp

commit 8249ad6b7678b2e68e9a0c3d8a7feffe538e80bd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 18 14:01:15 2014 -0700

    added function tracing.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 370e00eb3dfe86fa399ade3128a6f527a48587cb
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jun 2 16:22:44 2014 -0700

    create default if no topological map is found.

Src/C_BaseLib/DistributionMapping.cpp

commit 842af460fc5180e896ff327f4aee7184acc72cf6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 30 17:46:30 2014 -0700

    fixed a number of memory leaks

Src/C_AMRLib/Particles.H

commit fd3afe6338dba347031138b9a45a965c3ce4f909
Merge: cafc9be 9610d47
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri May 30 16:59:14 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cafc9be28609ce138805b9dfe9d905c4f4b4ae30
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9610d4720fe783d4d3d4450ef70e7c47f10f8bd3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 30 12:22:45 2014 -0700

    nodal_enforce.f90 --> nodal_enforce_dirichlet_rhs.f90

Src/LinearSolvers/F_MG/CMakeLists.txt

commit 66a529dd6fc56668fb92061ce213f7d7aa362776
Merge: 790804d a7870f7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 29 12:00:09 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 790804d5110e98ee1118ca0cbea66664003f288f
Author: Ann Almgren <asalmgren@lbl.gov>
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 a7870f703e2553923374ce50762ee0c6ddca9f7f
Author: Ann Almgren <asalmgren@lbl.gov>
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 09a73522d0dd310b36202e99f3de18e003244fda
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 28 16:31:00 2014 -0700

    Remove un-needed print statements.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit d47b8969fb90fcf3157cf344acdf55f1230947b3
Author: Ann Almgren <asalmgren@lbl.gov>
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 9d12510f508d644b0f4ca4d0666a6a493ece0035
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 28 11:39:48 2014 -0700

    reindex.

Src/C_BaseLib/DistributionMapping.cpp

commit 30796730fafb42cd4263f9494607a006d43a9c2e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9e41a766e5229c4a93a20d6d74444dd56a4fbb1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d4001301fef59c8085169d0591a5f469a0270120
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:38:19 2014 -0700

    removed cout.

Src/C_BaseLib/DistributionMapping.cpp

commit be00d0b13ecbe5411a8b8dd794ab41669f0b184b
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:36:12 2014 -0700

    added prof and commprof flags.

Tests/C_BaseLib/GNUmakefile

commit bfcc676719d02819632458919ed2a283b201e0a4
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:33:10 2014 -0700

    added tests.

Tests/C_BaseLib/tFB.cpp

commit 776258aadface133a28d8337145e7eb121ecaf40
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 22 13:02:08 2014 -0700

    added some profiling.

MiniApps/MultiGrid_C/main.cpp
Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 024a4bfe5159c0761105d5fe2f92df0c26cdbe0b
Author: beckner2 <vebeckner@lbl.gov>
Date:   Wed May 21 10:08:37 2014 -0700

    changes for intel compiler on cab.

Tools/C_mk/Make.Linux

commit a95f9495e2443338431a2d15394e8383a62f8d33
Author: Ann Almgren <asalmgren@lbl.gov>
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 8f84e0dc6147511d01933066da2892819092c20b
Author: Marc Day <MSDay@lbl.gov>
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 fbd3cdeee56921ec09824fd94cee7d16bc0e87c5
Merge: 8dbad2b 6536829
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 13 20:36:31 2014 -0700

    Resolve conflict in plotfile.f90

commit 8dbad2ba2e68484d5827d5d911216edae15fb4c4
Author: Marc Day <MSDay@lbl.gov>
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 6577b5921327668d03cd2377cd10ba8bb8387275
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue May 13 20:33:32 2014 -0700

    Allow longer variable names in plotfiles

Src/F_BaseLib/plotfile.f90

commit 6536829a575934f05de491fd5ebc342eb21a1cf8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 004936eb4aff856071a00771ee1d60109780dd1d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 13 11:17:07 2014 -0400

    update to add analysys plots to more tests

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 52e09b0db5c9e70512ee30a4ae0b1dbf887e458f
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 9e552352d1f78ff2c782afd3b96529635f856aa3
Merge: 8812a1b e4058b0
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue May 13 09:16:09 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8812a1b61f8d4bbdaa4e7fccb973bbf81ed89382
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue May 13 09:15:51 2014 -0400

    add analysis

Tools/RegressionTesting/Castro-SBU-tests.ini

commit e4058b0aa925fc1b1777f616f6cfcf653107925f
Merge: bbe297c b35aeac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon May 12 21:11:06 2014 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bbe297c8a88251fa3b2244f2cb3b7d897681789e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b35aeacae9c908dcef222959c00a1fa8690ee0e6
Author: ajnonaka <AJNonaka@lbl.gov>
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 591ed32fcb0bcd7ac20e412e632fd4c89e203265
Author: Michael Zingale <zingale@localhost.localdomain>
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 c2af5ab903c19c6eb6d48b615646a2866474d378
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 1f68712e544a80110649edd1c321e197d75ad465
Author: vince <vebeckner@lbl.gov>
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 84bfc1d0b071f8bf6fa864b774423d238598d842
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue May 6 19:01:32 2014 -0400

    the Castro tests we run at Stony Brook

Tools/RegressionTesting/Castro-SBU-tests.ini

commit 7620ba4940f3edbd74f8585b82a69e56567ea364
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 60e8126c7f36c647ac0eafcc457a0d0a2e339229
Author: Ann Almgren <asalmgren@lbl.gov>
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 806db98207fb0b25736b60a860952cc790497753
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 6 13:34:01 2014 -0700

    Remove some unneeded dependencies.

Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90

commit fdde9422495b0e07ab6a6fae58ed136faec29724
Merge: 8993142 0611941
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 6 09:40:45 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8993142c751c438871d82ed9845278270526c85d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 6 09:40:12 2014 -0700

    generalize make.defs to handle aliased gfortran versions

Tools/C_mk/Make.defs

commit 0611941a7cc2fe36cdb4282e1bc3813b168c95f0
Merge: 1155971 624e530
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon May 5 16:07:11 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1155971fde263323d75dd76b2b1b72388155de1e
Author: Ann Almgren <asalmgren@lbl.gov>
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 fe0aafebfe2778714fddcd87ae75c7a7853fe807
Author: Ann Almgren <asalmgren@lbl.gov>
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 624e530ada953c6fc0e69a7c7b8c75d377d8fe7e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aef0fba9a94273c344435e581db2acf32729382d
Author: Marc Day <MSDay@lbl.gov>
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 ba0344314ca8287010dafed685be2962df0ca03e
Merge: 3a45897 2880a33
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Apr 29 13:46:08 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3a45897a62a59b44bf41e068cdb8d6879376553f
Author: Ann Almgren <asalmgren@lbl.gov>
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 2880a3350fba9972f702b488f9606cb1f7fca136
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 98426666046fca27c0e71f552defe99ca404ee52
Author: ajnonaka <AJNonaka@lbl.gov>
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 847667795fccb6fdecbf3f38a33a01c5cddc07d1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b2bf12460856ae2dc5e5f1c4188be9c6c8f6c41c
Author: Ann Almgren <asalmgren@lbl.gov>
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 9bfc179861656c2fb4b110b41dbc64f6e028b863
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
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 844e679f607d5a05ad95106201a3003c12ddef13
Author: vince <vebeckner@lbl.gov>
Date:   Thu Apr 3 16:46:55 2014 -0700

    reworked reduction tracking.

Src/C_BaseLib/ParallelDescriptor.cpp

commit d470c62a3e647dae037e11c59ee2444295f4000a
Author: ajnonaka <AJNonaka@lbl.gov>
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 7e97e968f0b4e9d5f7c743be83da98684bb9b693
Author: vince <vebeckner@lbl.gov>
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 54fa42c1975eacbb9fdfa353fa8a255ab81eb116
Merge: 9c4b0ed 55b4fd6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:20:06 2014 -0700

    Merge branch 'master' into commprof

commit 9c4b0edc5caf4ac15106f5f25ce28deaad9d32e6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:18:25 2014 -0700

    unconst

Src/C_BaseLib/Profiler.H

commit 55b4fd6dcae04fe7a3d84a74135597f5f0aa71c6
Merge: e242f12 b6cb92f
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:14:58 2014 -0700

    streamretry tweaks.

commit e242f127f01ade794c884eff44d4fae144e9b9e4
Author: vince <vebeckner@lbl.gov>
Date:   Fri Mar 28 12:10:31 2014 -0700

    streamretry tweaks.

Src/C_BaseLib/Utility.cpp

commit b6cb92f13a7ad31f2280aa0b8e424dbfa2892626
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2f892b2b477965af58bc22e928815dbd15ae9fad
Author: ajnonaka <AJNonaka@lbl.gov>
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 ef33bfd3fa5eba180e630b9856e8fa4b2fbf68f6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:51 2014 -0700

    cleaning out cc_applyop

Src/LinearSolvers/F_MG/cc_applyop.f90

commit 9d9513c30a6a250d9a78c263639f354d651956b2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:46 2014 -0700

    add nodal_applyop.f90

Src/LinearSolvers/F_MG/GPackage.mak

commit d68b2cb0f36317aff90841a867b86342526f05e9
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 15:48:30 2014 -0700

    writing a nodal_applyop... wip

Src/LinearSolvers/F_MG/nodal_applyop.f90

commit c29e88eed2981934975495c542939c7d62be88b4
Merge: f9cbab9 8de9e37
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 09:57:17 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f9cbab9303c896b6a7a13706600501e1e78a9aca
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 09:57:03 2014 -0700

    make ml_cc_applyop public

Src/LinearSolvers/F_MG/cc_applyop.f90

commit 8de9e37220590417481609d034194f9acccf5403
Merge: c650d9d 76b20a3
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:16:10 2014 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c650d9dda0202457b3a67d3f15893773d44a9d96
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:15:56 2014 -0400

    spelling

Src/F_BaseLib/bl_constants.f90

commit 930b5843f9361cd703c5d5575304e3783c8f6860
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Mar 25 12:15:08 2014 -0400

    add TWELVTH and SEVEN12TH

Src/F_BaseLib/bl_constants.f90

commit 76b20a34a1b624c27118eef76d54f164ead7e964
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 25 08:36:52 2014 -0700

    remove a comment

Src/LinearSolvers/F_MG/ml_solve.f90

commit 2896d32dbee94d10fc4768002c2b466616cee3b9
Author: ajnonaka <AJNonaka@lbl.gov>
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 5ac8dc6b22848ea2d5dc427477b670701c997e91
Author: ajnonaka <AJNonaka@lbl.gov>
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 b205af32b3035d7e5a8fb9b3e73f8c8f9efc3ff5
Author: ajnonaka <AJNonaka@lbl.gov>
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 420282e49d4e7fa34359543af7a737ba230e0c6d
Merge: ac2f09c 574f92c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 20 15:44:35 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ac2f09c7ac84860ab749460f064dde45f3c17216
Author: ajnonaka <AJNonaka@lbl.gov>
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 574f92cb8b915a1bd650e9fb40a84787e91704ad
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 20 13:13:48 2014 -0700

    norm_cor is no longer used.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit ae99d7d271583b23e7de7c85162c259d9cc89ad5
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 e8b0b0310222475460c4eec1a74f09d12788ec3e
Author: ajnonaka <AJNonaka@lbl.gov>
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 0c5124136defc20b8a1a2f2d602b57b3d61cb732
Author: ajnonaka <AJNonaka@lbl.gov>
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 91e4e90ca5eafdce42b24c4340cb5bbad46cc3fa
Author: ajnonaka <AJNonaka@lbl.gov>
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 a0ac2509598025223717f7617c8662d24710162b
Merge: bafe109 89c279a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Mar 17 11:00:27 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bafe1091f3640e3a93176437881672e2a12dda03
Author: ajnonaka <AJNonaka@lbl.gov>
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 89c279a8adfb6acf773b7b8bffa4bf897e858797
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Mar 17 10:56:54 2014 -0700

    Uptick tag version number

Tools/CMake/BoxLib_Version.cmake

commit b7fba9e37c6b3c7c919d0404b0d82236543c2c9c
Author: Marc Day <MSDay@lbl.gov>
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 b3c5f821cf2e1d8fb357f90e8c6b7632df072a0e
Author: ajnonaka <AJNonaka@lbl.gov>
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 c9a0f494e0f55443e6a2aa04fc87b148d5cb6f5d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 21:31:55 2014 -0700

    Modified BSD license stuff.

README.txt
license.txt

commit af6511257bd2fa12c62e20eaa584fc0ca498905a
Author: Ann Almgren <asalmgren@lbl.gov>
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 36139c35f23843c485e8d7d4aba59d45e6e76bea
Author: ajnonaka <AJNonaka@lbl.gov>
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 851e7e6275786ad94a1832a3b11163249e0a9ee4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 16:01:20 2014 -0700

    cleanup only

Src/LinearSolvers/F_MG/ml_solve.f90

commit c1206820680faa9f79f9e6d5976a4afc683da90c
Author: ajnonaka <AJNonaka@lbl.gov>
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 51c492a8e9793d80118933cde3bf5cfb69b25d35
Author: ajnonaka <AJNonaka@lbl.gov>
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 0fb969583aaa2193db566ba21853ae5acc348a77
Merge: 33aa4a5 83efd74
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Mar 13 15:20:12 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 33aa4a56c4be5bf9cef891ba8d614eb953ae86e7
Author: Ann Almgren <asalmgren@lbl.gov>
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 83efd743c452e51fc0f282e3d5cacc34fb190a3c
Author: ajnonaka <AJNonaka@lbl.gov>
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 8a504d24d02caf13f0ccaab9dd3391a83a3e453b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 13:12:18 2014 -0700

    remove unnecessary optional arguments

Src/LinearSolvers/F_MG/ml_solve.f90

commit 43f4592923cca4126dc8c1aa572a10f776e56c68
Merge: 28d83c7 90d7292
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 13 13:02:59 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 28d83c763251935e91df687070f42fc3a26dc585
Author: ajnonaka <AJNonaka@lbl.gov>
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 90d7292de7fbed6eae69feb88f624e56fad89707
Author: Matthew Emmett <mwemmett@lbl.gov>
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 ad826963d62624663d62d033a377bbfbd668cd7a
Author: Matthew Emmett <mwemmett@lbl.gov>
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 7e6c9c51370bc583816a8d9f8f64e4607e1d2329
Merge: f0cf190 5d54592
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Mar 13 11:09:41 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f0cf190024b76b88e390302cd1b60eca4a7c2b83
Author: Matthew Emmett <mwemmett@lbl.gov>
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
Src/Python/src/boxlib_wrap_2.cpp
Src/Python/src/boxlib_wrap_3.cpp
Src/Python/swig/boxlib.i

commit 5d54592e5a1d0fd7feac13f86edfa9c6bb0a2e11
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date:   Wed Mar 12 16:55:16 2014 -0700

    index bug fix in new cc solver

Src/LinearSolvers/F_MG/ml_solve.f90

commit 280b35c2f787ab96654da5e1f29a5e578a2d7088
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 a1386031d5e627816ea659463471978de5f9a8c5
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 73acdae4e3faa158890160b73692840d2844b1f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 19dccdc0614d5072d029a613427bd5a9dd90b617
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 d11d0f70c80cd291526717bf66b83452771dffc4
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 621efa086864319739cc38a01da4c945c7784c3e
Author: ajnonaka <AJNonaka@lbl.gov>
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 cd1cfb81c81fdeff220959e27a5f2ae84b30cd8a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 11:22:19 2014 -0700

    cleanup only

Src/LinearSolvers/F_MG/mg.f90

commit 0c1530540a557561c04af1206395e2765e0c04b0
Author: ajnonaka <AJNonaka@lbl.gov>
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 753617c9a067bde0de1b0eac26dff79c3c8afb69
Merge: a1e774b 7e858fb
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Mar 11 10:30:06 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a1e774b982617e8729b126cbe8e8684e7dc42750
Author: ajnonaka <AJNonaka@lbl.gov>
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 7e858fb5462804b7c8112e511e0e516920a8c6b1
Merge: 8e46743 97bb852
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Tue Mar 11 10:15:06 2014 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8e46743441e9ea9ee3af2fcdcea9ebdfae83dfcf
Author: Matthew Emmett <mwemmett@lbl.gov>
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 84ab54fb249d24b829c95441bcc657c9515a8c60
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:58:24 2014 -0800

    merge with master.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 85313ab6a562a530ef462675282698bcf4048170
Merge: b384b52 97bb852
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:51:32 2014 -0800

    Merge branch 'master' into commprof

commit 97bb852391d58a78ac71deb92a157b9aeb6d3c3c
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 11:33:14 2014 -0800

    removed dumpi vars, they are now in Tools/C_mk.

MiniApps/FillBoundary/GNUmakefile

commit 315544bce0f8d78285b03aea3ccdfd9763498b60
Author: vince <vebeckner@lbl.gov>
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 2af23e2e8c1c0af6fdc03a6556b799dc6ba57884
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:30:29 2014 -0800

    new ncube code.

MiniApps/MultiGrid_C/main.cpp

commit c225104d6d66139a5f2b6cb73958eac285470abf
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:29:54 2014 -0800

    added ipm, dumpi, prof flags.  made more consistent with fillboundary.

MiniApps/MultiGrid_C/GNUmakefile

commit b384b52d53819207d07e1dc52dab73a09bfaa570
Merge: 2270d84 183ff1a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 10:13:41 2014 -0800

    merge with master.

commit 183ff1a4b0516fd63a8fc783402ca9214e65f4fa
Author: vince <vebeckner@lbl.gov>
Date:   Thu Mar 6 09:07:04 2014 -0800

    iop around error output.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 94d9e35c57146c553d0723345fa2a1551751e195
Author: vince <vebeckner@lbl.gov>
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 2270d84a365c63f383e9e870704cdf7b991cd6bb
Merge: ad588e7 673b77f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:33:59 2014 -0800

    merged with master.

commit ad588e7b6880b20fe46edb9eda0fd7173ec9e7f9
Merge: efc31b9 91c9388
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:29:37 2014 -0800

    about to merge the latest versions.

commit 673b77fb28c16179299812686362dd4d199050f8
Author: vince <vebeckner@lbl.gov>
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 fccc382e05e5ed328c5908297b4dd5621dcfb1ca
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 17:01:34 2014 -0800

    added new/old compiler flags and temporary dumpi support.

MiniApps/FillBoundary/GNUmakefile

commit c7df3a3d31e25ab717f885da2764ddb5505cc9a4
Merge: ac3e277 b0ae7df
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Wed Mar 5 17:59:39 2014 -0500

    Merge in sub-Chandra analysis routines in branch 'fsub_dev'

commit b0ae7df8aef42c1ca827ef1dbcd9c678fa474ca1
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 91c93885500965a9102cf142a12c57685f1f938b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 12:24:26 2014 -0800

    added run time.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit efc31b9eed9ee4ff5f175ddaacdfd1a63c987d15
Merge: 4d8cee8 18407cd
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:44:16 2014 -0800

    made these similar to the master branch versions.

commit 18407cd9b2e6884aa1fb7bd982b433fa6628e4ac
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:27:13 2014 -0800

    added other run sizes.

MiniApps/FillBoundary/qsub.ipm.bat

commit b2b52b5b02479089d726cd4634c4111dd29add31
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 5 11:23:11 2014 -0800

    changed filename.

MiniApps/MultiGrid_C/README

commit 8e098228fe54b1b94275defa9768181da6f7cbb6
Merge: 77ffa2a f1f05be
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Mar 5 10:37:43 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 77ffa2a31f6015ada939f22ab6de0204bf4cf704
Author: Matthew Emmett <mwemmett@lbl.gov>
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/base.py
Src/Python/pyboxlib/boxarray.py
Src/Python/pyboxlib/fab.py
Src/Python/pyboxlib/fabutils.py
Src/Python/pyboxlib/layout.py
Src/Python/pyboxlib/multifab.py
Src/Python/pyboxlib/plotfile.py
Src/Python/pyboxlib/pybl.py
Src/Python/pyboxlib/utils.py
Src/Python/src/blobjects.f90
Src/Python/src/blobjects.py
Src/Python/src/boxlib_numpy_c.c
Src/Python/src/boxlib_numpy_f.f90
Src/Python/src/fboxlib.f90
Src/Python/swig/boxlib.i
Src/Python/swig/numpy.i
Src/Python/tests/test-multifab.py

commit f1f05be3239ef04a2db8f7ad7d740d6152cc1e10
Author: Ann Almgren <asalmgren@lbl.gov>
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 6dda885f2ec8b83286c2e07e6334901f96c5315c
Author: Ann Almgren <asalmgren@lbl.gov>
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 614b6bde6bdef5d617a34e6cc84f9df8707cc76c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 3 10:33:53 2014 -0800

    Add suggested numbers of processors.

MiniApps/FillBoundary/README

commit 4d8cee8f6aabc1e4974fa4eee15e88287bdcbc5d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Mar 3 10:32:11 2014 -0800

    Add suggested runs.

MiniApps/FillBoundary/README

commit a6b1fd6c7946f3756a2c6d4fbb59a35d00142c1e
Author: vince <vebeckner@lbl.gov>
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 37b2e5ee8082d7a037bd508a8abc5eeb125b71e5
Author: vince <vebeckner@lbl.gov>
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 a22aa946fa6fa3fc5e53ddd97c11a790683067b6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Feb 28 12:23:57 2014 -0800

    files from commprof.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp
MiniApps/FillBoundary/README

commit c8681cd4b2c593c53f240fd4b4b67997a04c8204
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 21 00:12:33 2014 -0800

    test3d --> fbtest3d

MiniApps/FillBoundary/README

commit ebf052d71c583eaa503382f872e1741df51d66ed
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 20 18:03:51 2014 -0800

    squished into nested loops, added commprof tags.

MiniApps/FillBoundary/GNUmakefile
MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 301b6a76d02783dd7917742d15d9d0af0b2bdb72
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 20 17:59:54 2014 -0800

    removed some diagnostic output.

Src/C_BaseLib/DistributionMapping.cpp

commit d3c8ea29ecd39dffd89fea73035289af7560dd94
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 16:07:36 2014 -0800

    Fixed domain_hi.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 5d7a7cb33d7848e15e72ac051dea27129771d34a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 16:03:28 2014 -0800

    Fixed.

MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp

commit 6746751707b8d39d2e4af505e31dbc6fbc1e5639
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 15:50:30 2014 -0800

    Added info on how to build and run the code.

MiniApps/FillBoundary/README

commit fd1cbfa05c97d7747c080e87f5620d8757e69263
Merge: a52f043 a89e7c5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Feb 20 15:40:41 2014 -0800

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit a52f0438c858e35a562b7991d84721d48a36bcdb
Author: Ann Almgren <asalmgren@lbl.gov>
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 a89e7c545fa3c3771e00b2f0344fa3391b428b04
Author: vince <vebeckner@lbl.gov>
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 0a3d1b2bf80eca0bf7fe6d575b3adc085230d510
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Feb 20 17:48:32 2014 -0500

    allow for 2 extra build directories

Tools/RegressionTesting/testnew.py

commit ceb0ad6f5c3ce84dc78bf7d1b662079c341fe817
Merge: 3e5c6ca ee6e0d0
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 19 10:23:28 2014 -0800

    Merge branch 'master' into commprof

commit ee6e0d0198d459abb58d24d5f93bfcbb9f93d478
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 d78430667cb6bb3245d58952c41eed0dd6dd3941
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 3e5c6ca160a72309115ae06b133108d6263bcab4
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 18 17:33:39 2014 -0800

    added enum num.

Src/C_BaseLib/Profiler.H

commit d70eb8b880c8edd499630b243819261a48b5be41
Author: lijewski <mjlijewski@lbl.gov>
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 aff8f6098f5dd3e41c4ae0706cb4c8c885c1ff94
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 12 15:59:32 2014 -0800

    Uptick version

Tools/CMake/BoxLib_Version.cmake

commit 3838bd1d9d41f00969d57d4426f384c7122daf45
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Feb 12 15:58:13 2014 -0800

    Test mulitcomp

Tests/C_BaseLib/tMF.cpp

commit bd937ca0c8f098a2d8fc71e30bfe6c2ba4e1ff2d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 12:59:48 2014 -0800

    added timer for commstats flushing.

Src/C_BaseLib/Profiler.cpp

commit 9713a792faa33567defea08beae38572f90aa6ca
Author: vince <vebeckner@lbl.gov>
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 ced059bd30dd6daa6cdca511c0203d7e4aa98932
Merge: 2cc0692 9a4f8d7
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:43:05 2014 -0800

    fix merge conflict.

commit 2cc06927e76ee01d6b4e39571e2b8ae9561ebf4c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 12 11:28:57 2014 -0800

    added -DDEBUG flag

Tools/C_mk/Make.defs

commit 65ed43095024a147aae9a64c435abb2cbb790666
Author: vince <vebeckner@lbl.gov>
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 e4c6d4b8e9dc470ba2696e5528adfed7918ba3cf
Author: vince <vebeckner@lbl.gov>
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 9a4f8d779691c93742e78eae2111ee4759c3fe06
Author: cmalone <malone@ucolick.org>
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 930a8e0df84016e9e5c8cf86f317abe8d2b9c1fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 5 14:16:21 2014 -0800

    regression test script: added diff to restart test

Tools/RegressionTesting/testnew.py

commit e80e8c4028d646a3a58014adbef9ce366e7064b0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d19b4a8f472c4125dc2b809aa8f0ba99205dc83b
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 4 14:01:37 2014 -0800

    mpi lib fix for mothra.

Tools/C_mk/Make.mpi

commit 8e70fe6780bfb011d78a484c6f673cfc6c38c987
Author: lijewski <mjlijewski@lbl.gov>
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 708dc04bb9abf0db801a72bf4bb9cc341ff06c44
Author: lijewski <mjlijewski@lbl.gov>
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 c475e5d32558e39e4382cc6e9550fff2bb07396c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 30 14:13:34 2014 -0800

    Merged Vince's stream retry idea into Checkpoint().

Src/C_AMRLib/Particles.H

commit 8297fe3bd5f3e94dc4402d3d797139ab69b5b82c
Author: lijewski <mjlijewski@lbl.gov>
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 a4be50740f6b0e32480188a11d7b98a7fd7434ba
Merge: 02662f5 092ada2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 29 10:02:23 2014 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 02662f59be3da08a969c262284063d635ac5d556
Author: Marc Day <MSDay@lbl.gov>
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 092ada2a678797f97476fd48b11b57b20cb33f3d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 27 14:14:19 2014 -0800

    More aggressize free()ing of memory in RedistributeMPI().

Src/C_AMRLib/Particles.H

commit d3248b2cc7fc72208f3d992352f1ffd649a2ffbb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 27 14:13:49 2014 -0800

    Increased fabarray.maxcomp to 25.

Src/C_BaseLib/FabArray.cpp

commit 80b507e1d9b4356cb1782b126402ca6586fe4cb7
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 24 16:12:23 2014 -0800

    removed output.

Src/C_AMRLib/Amr.cpp

commit a9cdc809a68efd192d3a956f5d53887cda67a590
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
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 d414d85af44c6acb875895d1ade7a0f82057e725
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 24 11:52:44 2014 -0800

    comment.

Src/C_AMRLib/Amr.cpp

commit a33e841f4dc1a159572ffb96ae3bece3de7ae6d8
Merge: 2628181 0ab4eed
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:26:38 2014 -0800

    Merge branch 'master' into streamretry

commit 0ab4eed051c1abfecfb9227efce74974bee055f1
Merge: 3175d75 4badd32
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:26:18 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2628181376859157ec90443af91320fc86b91243
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 15:25:33 2014 -0800

    less verbosity.

Src/C_AMRLib/Amr.cpp

commit 976e725cabc2d0075a3fe4201868c5322a0241d7
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 14:30:29 2014 -0800

    changed temp file verbose output.

Src/C_AMRLib/Amr.cpp

commit 23e13c544ed3dd8680d93a7cfb8ebe35bb36fabd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 23 13:55:44 2014 -0800

    more stream information on retry.

Src/C_BaseLib/Utility.cpp

commit 4badd322415e97c58643c2f492833de43d584a9f
Merge: d738255 92e5f0a
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 23 14:32:28 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d7382554e665de39d9feead38d6685677d797432
Author: Adam M. Jacobs <adam.jacobs@stonybrook.edu>
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 3e2b61f3b8b8c06f03d3b2e9fcf6a50256dfc9e7
Author: vince <vebeckner@lbl.gov>
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 92e5f0ab95630a9e4e06eb2520fb1358993f97bb
Author: lijewski <mjlijewski@lbl.gov>
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 3175d75698ad37e7b12598d4d299a0233d887ecc
Author: vince <vebeckner@lbl.gov>
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 c4d7c89cb214f7b3509e965c6fe2e47b53aa5a0d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 16 14:10:50 2014 -0800

    delay reset of fab format.

Src/C_AMRLib/Amr.cpp

commit e19ed6d6cda7128de09f0fc30ca1a2bf05b0703f
Author: Ann Almgren <asalmgren@lbl.gov>
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 3368f5d092bebca7496995e964db19440da74a6c
Author: lijewski <mjlijewski@lbl.gov>
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 0abf5e1f6a3ac92e832ca9d9a2cf69c361580331
Merge: ba43b6f 9f35cbd
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 9 11:25:00 2014 -0800

    Merge branch 'master' into commprof

commit 9f35cbdba8af1621e8bd03a5ef24482498f8f3bb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 7 09:48:07 2014 -0800

    A little simplification.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit a2bf53a75d523f73cb131e1b120f764ea998f8cf
Author: lijewski <mjlijewski@lbl.gov>
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 e70a4064a9edfac32a2220d66b4b245ffd492a5a
Author: lijewski <mjlijewski@lbl.gov>
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 22d40369450ae343b7d0bb4eadec1d4c25023f57
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 12:34:00 2014 -0800

    Always use F90 solvers.

Tests/LinearSolvers/C_CellMG/MacOperator.cpp

commit 94b782a883ad5fe2a56debfb9c7deb24be8253a1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 6 12:13:53 2014 -0800

    Shut up compiler about "possible" uninitilized data.

Src/F_BaseLib/bc.f90

commit 400f2336a7e3ce51563312bb9fffd4ecb481a1b7
Merge: 60cd4dd 92038f8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 2 15:22:18 2014 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 60cd4ddb7d3c2ee5629d2262866cfa03008fb22d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 2 15:22:02 2014 -0800

    add USE_WBAR option

Tools/C_mk/Make.defs

commit 92038f8c44c4c401e379cdfbb8a3e1c78a601a9a
Merge: 963f1fa f134c10
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 2 17:03:26 2014 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 963f1fa0f90f74454fad49bd534aab05ccb9da62
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Jan 2 17:02:19 2014 -0500

    Updated GMakeMPI.mak from jaguar to titan.

Tools/F_mk/GMakeMPI.mak

commit f134c104487edfb0ea19089600af5f61a46c3e20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2c9f45dd34b41685cff153b3bef83541f9169bab
Author: lijewski <mjlijewski@lbl.gov>
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 a48270bef62994de9f694dc2131d0861a69e5357
Author: lijewski <mjlijewski@lbl.gov>
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 85ffb49aff87078f1f93933e79d29b3644cc920b
Author: lijewski <mjlijewski@lbl.gov>
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 c4a4846323cb3ebdce3d473caeec639a79b54067
Author: lijewski <mjlijewski@lbl.gov>
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 c1efda8cf11cf204c20e36d81c8b09bac1455099
Author: lijewski <mjlijewski@lbl.gov>
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 f3905a40675656a63b3040f0922d21c4635b7eec
Author: ajnonaka <AJNonaka@lbl.gov>
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 d0192f898f6aef7b1b377e8d6c5e28a45cb7f8f4
Merge: dc96c7f c0f8756
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Dec 19 15:36:20 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c0f8756be27cf5ccda21930538af611c4f4a4b77
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 19 14:08:01 2013 -0800

    Forgot to remove a debug statement.

Src/C_BaseLib/FabArray.cpp

commit 951475a20f2927b9643734c544c99b90f4035343
Merge: 52b1da2 036b811
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 19 14:03:34 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 52b1da2cb554d70eb5a62cc301b1a82a16a26abb
Author: lijewski <mjlijewski@lbl.gov>
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 036b8110b5380c73b7c7685eac287f30fce2d331
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 19 13:11:39 2013 -0800

    fixed comment

Src/C_BaseLib/FabArray.H

commit 3a57e878f4b3a1bc67ada5cc88d8714455e1d6d7
Author: lijewski <mjlijewski@lbl.gov>
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 55a33339fa3133a6c0b203dfcd89c11b888c04dc
Author: lijewski <mjlijewski@lbl.gov>
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 0ea8d45f2b26cce6d85c5127f7b5a5bb5345fdca
Author: lijewski <mjlijewski@lbl.gov>
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 580547bfc1ec131bb521b5c889d894471e057453
Author: lijewski <mjlijewski@lbl.gov>
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 901d6dc73edc16ffb6cb8392c2479c8a560f48b6
Author: lijewski <mjlijewski@lbl.gov>
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 ddacb5d444a0c6b833060430d14c852c7f688e2b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 17 14:05:29 2013 -0800

    Some cleanup.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit e0d0c3f30a36ac465306b038c5dd74e26ec3906e
Author: lijewski <mjlijewski@lbl.gov>
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 dc96c7fa4d7c9b1f52e451babddaa2411d6ad56b
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Dec 17 10:19:35 2013 -0800

    Double colon rule so we can extend if necessary

Tools/C_mk/Make.rules

commit 8a93e76ad27efd0da9166251617e834befdb11df
Author: lijewski <mjlijewski@lbl.gov>
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 b12e6036ee8a2b5749eb87772b111be2c2f8a7e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 16:41:53 2013 -0800

    Cleaned up some verbose output.

Src/C_AMRLib/Amr.cpp

commit c1756e480a5a65dfb814eabd50dbe24a41174d23
Author: lijewski <mjlijewski@lbl.gov>
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 ba43b6f0561023989f9d12412ea773861368344f
Merge: ea6ac6e 16e48dd
Author: vince <vebeckner@lbl.gov>
Date:   Mon Dec 16 15:12:44 2013 -0800

    Merge branch 'master' into commprof

commit 16e48dda78ae5762532131fe06cd288dfe134db8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 16 13:58:19 2013 -0800

    Squeezed out some more memory from the hash tables.

Src/C_BaseLib/BoxArray.cpp

commit 8a9ed72a2f1877466e2da1f370867936fff9c3f1
Author: lijewski <mjlijewski@lbl.gov>
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 9b446e73de3cb3d678266d08162dc3e4c56b0f5a
Author: Ann Almgren <asalmgren@lbl.gov>
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 98a75c520dcd9c5eaf102f9c154dd8d992d5383e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 11:00:22 2013 -0800

    More BoxHash statistics.

Src/C_BaseLib/BoxArray.cpp

commit 87103e9182f3f0799f651179c5ccf8e4213136bd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 10:40:59 2013 -0800

    Added a clear_hash_bin().  AddBox() calls intersections() ...

Src/C_AMRLib/FluxRegister.cpp

commit 3ac81d0aee2a8a93580b183455b6dc7577c753c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 13 10:40:40 2013 -0800

    Added a clear_hash_bin().

Src/C_AMRLib/TagBox.cpp

commit ac3e27715461f914ab48f12b7b757a0dba7c9274
Merge: 184f40c 3d1eec2
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Dec 13 12:08:09 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 184f40c8dc28fc5c35afd1996eedba4449bca8c9
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Dec 13 12:07:45 2013 -0500

    don't require --infile1 --infile2

fcompare.f90

commit ee143ad65e95d61808926415b4cdc82757e77c07
Merge: 966b9c3 aba95cb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 21:06:01 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 966b9c33af81b018baff0f53a2b80ae336f4fd5b
Author: Ann Almgren <asalmgren@lbl.gov>
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 aba95cb1f29cc1a3ac9e8ebcf7c6b9e914171ac7
Author: lijewski <mjlijewski@lbl.gov>
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 f6700a83e939537246ec1d9fb723a273099da1e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 14:42:03 2013 -0800

    Remove left over print statement.

Src/C_AMRLib/Particles.H

commit 3282494988f083c091922f81b689214705341e2e
Merge: 82fa159 c618d86
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 12 14:37:29 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 82fa1590938ddfb12079a915f8a058b3a41664a4
Author: Ann Almgren <asalmgren@lbl.gov>
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 c618d86faaf450d1da935ddb795a85bcbbb161b6
Merge: ead2de4 6307886
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 12 13:39:00 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ead2de470709d356965172bef56427dd653aa190
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 12 13:38:24 2013 -0800

    Added more debugging statistics to box hash bin code.

Src/C_BaseLib/BoxArray.cpp

commit 63078863335e258f0e7be653e38cd75801a8ec5d
Author: Ann Almgren <asalmgren@lbl.gov>
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 186f011e6d8a3b8c85d9c0bd06aed0adcc2d214d
Author: lijewski <mjlijewski@lbl.gov>
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 96c86b1009012b14dece1e7b5b369e6097539720
Author: lijewski <mjlijewski@lbl.gov>
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 4f52285789d34f7a7ef6fa4fa1c12d7ecf226b45
Merge: 76577dd 72e2483
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 17:56:23 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 76577ddfb4a57cd1cf39dae2e0f46946a6a9b57d
Author: lijewski <mjlijewski@lbl.gov>
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 72e2483ee75a520b27348d4f7f23a9307ae79da9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 10 17:21:40 2013 -0800

    Removed commented line.

Src/C_AMRLib/Particles.H

commit 8f4cd9d9e6ecb2f73b1545912cf77078c465e0d8
Author: Ann Almgren <asalmgren@lbl.gov>
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 a8b90f277d99a1c5c603f1d9127e0c2694a6e6a7
Author: Ann Almgren <asalmgren@lbl.gov>
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 e63cc29b01366154469a2607fe41d7e624a366fb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 15:25:06 2013 -0800

    Be a little more aggressive clearing box_hash_bin.

Src/F_BaseLib/layout.f90

commit 6a921d778203b2f003746be0ab786ec121b18c5d
Author: lijewski <mjlijewski@lbl.gov>
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 a830de9f74994c7991ac6a873e2c898438340ebe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Dec 10 12:53:04 2013 -0800

    Some cleanup.

Src/C_BaseLib/BoxArray.cpp

commit b3ed807387435003753ef4d17f91899e4047dc05
Author: lijewski <mjlijewski@lbl.gov>
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 e5553e88b4fff1d306042abbea28fa8891c7c8f5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:51:31 2013 -0800

    Increased verbosity level at which some debug output appears.

Src/F_BaseLib/layout.f90

commit 43690fc09c81c1b85eba4afa7e9f8e30ef2305a2
Author: lijewski <mjlijewski@lbl.gov>
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 2d52f7549da9f2eb5d782c2df4d69263c0d5067a
Author: lijewski <mjlijewski@lbl.gov>
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 42f33bda143cfa80bf25af8d0d992c14958c4b2b
Author: lijewski <mjlijewski@lbl.gov>
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 57b0b76dc0f5670a59075254a342092a24022bfd
Author: lijewski <mjlijewski@lbl.gov>
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 09da45f67fd950f115bd1aefe398085110131b60
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:04:11 2013 -0800

    Merged in call to clear_hash_bin().

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit c9afebd27b0195194b58605cea387cd64a5e1e6f
Author: lijewski <mjlijewski@lbl.gov>
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 d8ae81efd1c0067ca3dc809ce8a513d2a6f06b9c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 21:02:39 2013 -0800

    Removed some debugging output.

Src/F_BaseLib/layout.f90

commit 92b8d0981e68b526872ba9f386b2c96a653277a4
Author: lijewski <mjlijewski@lbl.gov>
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 dc5a6505dfc730830b0b66a2a5b301c9aee221e9
Author: lijewski <mjlijewski@lbl.gov>
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 d3a114acd1f426bb10dba01de773a3ba762d6f39
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 14:37:31 2013 -0800

    Squeezed out some memory from the boxarray hash.

Src/F_BaseLib/layout.f90

commit 39b4f9341a8e2c2a4e7f32b63ff5cd36c42e106a
Author: lijewski <mjlijewski@lbl.gov>
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 e87625fd1ab0450c0fc09400fc6cf6b7b1957584
Author: lijewski <mjlijewski@lbl.gov>
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 2438c4ea3a94283c7ef947a39cfbda79452b479c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:44:37 2013 -0800

    Some cleanup.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit e53944791524081eb25f7770dd78d351d97f5883
Merge: 852d9e4 a776235
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 9 10:22:22 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 852d9e455df3d80aae2ce570019a7ba376bfcbe2
Author: lijewski <mjlijewski@lbl.gov>
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 6884575e39905e5021f0220e843b7f27cc958f33
Author: lijewski <mjlijewski@lbl.gov>
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 a776235518314d4c6c7638142ad27d5f1e6bc046
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Dec 7 12:12:18 2013 -0800

    Add sanity checks and comments in ParticleContainer::addOneParticle()

Src/C_AMRLib/Particles.H

commit 0b15c631990e9ec7e8b18a537e999f8cf8f6bdc8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 6 14:14:47 2013 -0800

    Fix typo.

Src/C_BaseLib/FabArray.cpp

commit 21e3ce87ac295283dcc01af236f5db862b834048
Merge: 74c2f5e 2432e61
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 6 13:54:51 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 74c2f5e062265e42baf305b4b830f79148b9e7cc
Author: lijewski <mjlijewski@lbl.gov>
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 2432e616b8ea6b69b474bad4ce3450818239c49e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 4 14:01:25 2013 -0800

    Fix coefficients in tridiag.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit db0609700fa3500334a0c6584f9b2e51249b4e87
Merge: d879997 ff7ba31
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 3 16:20:23 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d879997299619919ee0bb1a3527dd37d5b633554
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 3 16:20:11 2013 -0800

    Add new files to Make.package

Src/C_BaseLib/Make.package

commit e39feff5aaac3ab95371d89a35ef6b44d45414d0
Author: Ann Almgren <asalmgren@lbl.gov>
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 ff7ba31d96da74460f773457795a99e08cacc6c1
Merge: 4dc4b04 48d4925
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 21:27:22 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4dc4b042f8ac1522a993dc41c547735cb174b17e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 48d49251af16f1f9b8965b59f75ab53e169e5090
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:44:47 2013 -0800

    DatasetClient.H no longer lives in this directory.

Src/C_AMRLib/CMakeLists.txt

commit 4b79909175406e318dbbbab16c0bd1bae6a129d3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:22:35 2013 -0800

    Add nodal_stencil_apply.f90 to CMakeLists.txt

Src/LinearSolvers/F_MG/CMakeLists.txt

commit 34258cdc425a5e25afb69967a333eeab0c810437
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:19:02 2013 -0800

    Add compute_defet.f90 to CMakeLists.txt

Src/LinearSolvers/F_MG/CMakeLists.txt

commit 0f4d2e002d45e79b3902c29db49b214cd711203f
Merge: d03cdd7 6a8e4a1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 2 13:01:23 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d03cdd725675d1ee7f62df47f6e3e4e440be283d
Author: Ann Almgren <asalmgren@lbl.gov>
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 6a8e4a1dc054e5622f556be76979d4f3029d687c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f19c451ade81e18e40c24bc27937ab3263a39b6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 10:40:09 2013 -0800

    fixed OMP bugs

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit b6b4e54748391f9ec31748f2c6b33c315af83b37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 2 10:06:46 2013 -0800

    fixed an OMP bug

Src/F_BaseLib/create_umac_grown.f90

commit 37995cefca056ad15f620f261e6885e4ebdb8684
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cf76f87a8d1881347152ed896781126c15127b9e
Author: lijewski <mjlijewski@lbl.gov>
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 ec52c91f8a42181a4d7f0ffaeca8c3a3bf421509
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 38bb48e3ca57f9580460c7f911cffb7e6939e286
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f7de4378da95de1500665414cbc527ca469e19cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 26 14:34:33 2013 -0800

    fixed a minor OMP problem

Src/C_BaseLib/BaseFab.H

commit 4198681daad6aaffa92b8441435b2f0b4d431b5c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d4627b1704fb3e3f4533e495627e0273b1fbceeb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 25 20:00:51 2013 -0800

    Some OMP fixes.

Src/LinearSolvers/F_MG/ml_nd.f90

commit be5ae8effbbc10c02a58410da301885e69393e63
Merge: 714b43a 8b68cb9
Author: Ann Almgren <asalmgren@lbl.gov>
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 714b43add1ad03ac378fa1bfd21f4d4e85beb499
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 25 19:33:00 2013 -0800

    Fix indices in nodal_stencil_norm.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 8b68cb9fc77e80bb5128280f750f17943616ef52
Author: lijewski <mjlijewski@lbl.gov>
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 d6f3af2df2a9c8ec4578d3763372eb49c8a093d8
Author: Ann Almgren <asalmgren@lbl.gov>
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 4d0bc68c9f74e6b6de8dd331c06add2881de3b27
Author: Ann Almgren <asalmgren@lbl.gov>
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 08b269fc1acc239e8fd6cc361139623bc914610d
Author: Ann Almgren <asalmgren@lbl.gov>
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 ea6ac6e9e57d61191b370a037123aa529eebbd50
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 25 14:34:15 2013 -0800

    reset strategy fix.

Src/C_BaseLib/DistributionMapping.cpp

commit 53bc6d8a4a7f7c104ec2d0dbee6435a47905a9e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 25 13:32:00 2013 -0800

    fixed a bug in nodal stencil

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 0791d360a1636992fc9094c42e662acef327a765
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 daa3d2f96f4ddf944c30ead4744e8c9bbed0cc4b
Author: lijewski <mjlijewski@lbl.gov>
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 787c846cec8a7a8585ec8c78b810feb42822706e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 15:42:22 2013 -0800

    Fixed typo.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit cf587c51d9381865da76aff08429550e7074c3ef
Merge: ccfb9b9 fbea799
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 15:35:42 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ccfb9b9f0b428edca5d8a06774d4c20d280377bb
Author: Ann Almgren <asalmgren@lbl.gov>
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 fbea799d248d80ba5ace093f105c50cac8d8fd7f
Merge: a18f76a 3d69251
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 22 12:40:04 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a18f76a8d5ff8cccc3722feba0ddaaf4721f805d
Author: lijewski <mjlijewski@lbl.gov>
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 3d69251cd06aabb444e19cc34ab8664cee4eb643
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 11:16:25 2013 -0800

    Only have diagonalize=true for nodal solve.

Src/LinearSolvers/F_MG/itsol.f90

commit 3f52768a9cfed4774196c58e4b3f4e6ac74206f8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 11:09:09 2013 -0800

    No longer pass ns into mg_tower_build.

Tutorials/HeatEquation_EX5_F/advance.f90

commit 0490638368ba9a892df33ef0df8652e017055de6
Author: Ann Almgren <asalmgren@lbl.gov>
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 4cf8374aabd4cc88155915292bb932f2de6f503f
Author: lijewski <mjlijewski@lbl.gov>
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 6078399e2aca5b8928bcafdf869697e0d8885925
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 10:43:41 2013 -0800

    ns --> mgt%ns

Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90

commit 5d0367a157e2526919de47a0e0b93ddffe38336d
Author: Ann Almgren <asalmgren@lbl.gov>
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 ef86291d1ab894f7069850e3745f1ffb5a1715e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 22 10:16:35 2013 -0800

    Use mgt%ns, not ns.

Src/LinearSolvers/F_MG/mg.f90

commit 6092c9376334ec131e1f1ebb29193ddea53d0a6a
Author: Ann Almgren <asalmgren@lbl.gov>
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 99fbf93cbb622557df6f7023ce0837e965c9784b
Merge: 389500a 0514716
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 21 16:40:12 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 389500a41f9577daa0115084d3d8a703a327bef0
Author: Ann Almgren <asalmgren@lbl.gov>
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 8aeb97027a30d621fbbd17879fab2d4a5d109f4d
Author: Ann Almgren <asalmgren@lbl.gov>
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 d101569b6356c97fdbf0906fc044e0adb243d5bb
Author: Ann Almgren <asalmgren@lbl.gov>
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 73cf58c59d06ea17ddf8d8bc7b7f283bda627c87
Author: Ann Almgren <asalmgren@lbl.gov>
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 05147165711f6ca554ee7741ae053aced57300b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 21 13:06:38 2013 -0800

    fixed makefile in F_MG for C++ codes

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 5323d990fe0733e36f19ab246306616e4a0de632
Author: Ann Almgren <asalmgren@lbl.gov>
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/mg_tower_smoother.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 1c3450cfc8b8a4cd1e3b3431a565fa6e4bd99911
Author: Ann Almgren <asalmgren@lbl.gov>
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 b18d247295779459a946e8416a32a9bcf9dc8db7
Merge: 0d0235a a8fbdd0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:37:05 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0d0235aed7abcd5946f93603e72142fd7d8ccb59
Author: Ann Almgren <asalmgren@lbl.gov>
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 53fa31fdbb5a2590075c633df00d7e4e23df0a41
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:36:08 2013 -0800

    The filest are listed in GNUmakefile instead.

Tests/LinearSolvers/F_MG/GPackage.mak

commit 9923d1840ac3dd97f4367e2020f56f693954d779
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:33:32 2013 -0800

    Get rid of Jacobi options within smoothers.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 12deadec217e7460f23c7c0c4b62bf34fe604e25
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 12:33:12 2013 -0800

    Better formatting.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 5692c902b30221d8d4cf1723313d1e21a29568d1
Author: Ann Almgren <asalmgren@lbl.gov>
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 bc518d99dccf0c9dec73ece74a3b251c0b38a5a3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 20 11:28:47 2013 -0800

    Get rid of Jacobi smoother.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit a8fbdd06fbcf8a6d9cc60e5f6abc4ebc665513ac
Author: lijewski <mjlijewski@lbl.gov>
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 53769811ca7573962452429875a8f7b35f83aee0
Author: lijewski <mjlijewski@lbl.gov>
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 149b79551780f18e0d75ade754af75e4878dc96d
Author: lijewski <mjlijewski@lbl.gov>
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 7eaf38ec5b62ce88a288f8ca258c873c2108bad0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 18 14:13:54 2013 -0800

    A little cleanup.

Tests/C_BaseLib/tMF.cpp

commit 0b59f677575740b67530dd5da1528cc7bb0c2481
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 18 14:10:38 2013 -0800

    This test is now a simple example of how to reduce a std::map<int,Real>
    across CPUs.

Tests/C_BaseLib/tMF.cpp

commit 3196d1ffad20ca144ca7b41bc29e233b420771b2
Author: Ann Almgren <asalmgren@lbl.gov>
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 2e2c1600228eabc54e2351ad544a0462dbfca273
Author: vince <vebeckner@lbl.gov>
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 820c6e30739548b2f3adc12e42408109f263adac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3d1eec2561b843941eac0d5585d93ec6d0e9ee9c
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Nov 12 18:23:52 2013 -0800

    remove debug print statements

MAESTRO_xrb/fbuoyancy.f90

commit fa8332ea9fd994ea558ea579f8c8213a659a28f2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 12 16:18:17 2013 -0800

    We no longer use mgt%st

Src/LinearSolvers/F_MG/mg_tower.f90

commit ea13ae1dbd8e9c1b959148281a4d1d0d2f5cfe10
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Nov 12 15:21:44 2013 -0800

    get this compiling again

MAESTRO_xrb/fbuoyancy.f90

commit 17342cd7ea9f5bc2d470dc1acb6a875c206e46e4
Author: Marc Day <MSDay@lbl.gov>
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 abb197b36d43faca9f81c46c16d7294218a82f6d
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 11 12:00:18 2013 -0800

    removed print.

Tests/IOBenchmark/IOTest.cpp

commit 1dd4f1b0d2d7c6b4568cd6e3f63dfa588317f3c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 338b4262680a8d4899f235b0e742eb38021e83bd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 11 10:07:40 2013 -0800

    Fix to quiet PGI compiler.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ffa918aff478b3927962df85d14ab2ad9f41311c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 004d96a3efbfe5aa98ca6cabb189b16ffb6d10ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 697c573cf339bdabb1f1c3fa8dd554085130ea2b
Merge: edc50bc 365d0af
Author: vince <vebeckner@lbl.gov>
Date:   Mon Nov 4 12:09:31 2013 -0800

    Merge branch 'master' into commprof

commit 99780b9ce4a005cb5a6becd312db6ddaa14ae893
Author: Chris Malone <malone@ucolick.org>
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 edc50bc8102379ce86236cf8aeb99c9f07696f82
Merge: 2cfa64c bfd8742
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 31 11:23:55 2013 -0700

    Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof

commit 365d0af7e4df9787cfe1cc48947eb92c62331fc4
Merge: e0bc953 993d6a3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 29 16:30:21 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e0bc9532a3d649035e10c4b7073766fbf0f75600
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 29 16:30:00 2013 -0700

    fixed parallel bug for fabs and multifabs.

Src/Extern/amrdata/AmrData.cpp

commit 64c713c2c460331412d2b6c213ccf254932dcd59
Author: Chris Malone <malone@ucolick.org>
Date:   Mon Oct 28 17:02:11 2013 -0400

    actually add a usage statement

MAESTRO_xrb/frates.f90

commit 993d6a3be68eb3d16c02be75fc3a956cb4da9dee
Merge: 9afecb0 d53e06b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 28 09:23:19 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d53e06b7fe4ed8a655b10e3e800dd77e0366abda
Author: lijewski <mjlijewski@lbl.gov>
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 9afecb0e925fbdf962069dfd5f462340840c196d
Author: lijewski <mjlijewski@lbl.gov>
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 2cfa64c63f5bd79d1c5aae5f7fd1fc36b6ba3166
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 25 11:42:22 2013 -0700

    close file.

Src/C_BaseLib/VisMF.cpp

commit f508df09f3382c5d6ea2e5133176bdafe2f4cfb1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 25 11:42:05 2013 -0700

    close file.

Src/C_BaseLib/DistributionMapping.cpp

commit bfd874231501a484aa38d9e4fecfc74299ae3b3a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Oct 24 15:28:35 2013 -0700

    hopper test.

Src/C_BaseLib/DistributionMapping.cpp

commit 2ed1278b8bca1268868d4cf6a19ac125b1b411d9
Author: Marc Day <MSDay@lbl.gov>
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 3e179dd23ddb5c14d4232f6d98ae5cb7433ec3b9
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 15:54:22 2013 -0700

    hopper test.

Src/C_BaseLib/DistributionMapping.cpp

commit 8ca8c28c5c51ccecb7bea1fd8d170920bfe1794f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 15:14:29 2013 -0700

    procname.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 7536fdae3151b43c7d36a0161a2737e3303352bb
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 14:51:30 2013 -0700

    no report for zero perfmon procs.

Src/C_BaseLib/ParallelDescriptor.cpp

commit e43b4cfd470ab15eeb9fa27747d61e76b87b8016
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 23 14:30:38 2013 -0700

    hopper fix.

Src/C_BaseLib/Profiler.cpp

commit e396c403efbad0d00e657ea1400fb63d1e404b5d
Author: vince <vebeckner@lbl.gov>
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 4a8d665c37f67e07d21255f06c4b450b6d41db8c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 21 09:58:46 2013 -0700

    No more DatasetClient.cpp in CMakeList...

Src/C_AMRLib/CMakeLists.txt

commit 9adfbcc7f69f6f7e5483230b2f35d915d4f49d9e
Merge: b6db08b 43acee0
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:16:25 2013 -0700

    Merge branch 'master' into commprof

commit 43acee06e0795cf68aca91c64575a33e9191cb8c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:12:47 2013 -0700

    added arrayview support.

Tools/C_mk/Make.defs

commit 839c7f3e8a12c6fa9cde1844c61dcfd8f77a2950
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 18 15:10:50 2013 -0700

    added arrayview support.

Src/C_AMRLib/DatasetClient.H
Src/C_AMRLib/DatasetClient.cpp

commit b6db08b4c9193a8b55b80b1b5740c4bedecaae53
Author: vince <vebeckner@lbl.gov>
Date:   Tue Oct 15 14:22:50 2013 -0700

    more proximity mapping.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit ad5a3b4504cbb64dd035bdc120e21fc4be852178
Merge: e338a51 6a51cba
Author: vince <vebeckner@lbl.gov>
Date:   Fri Oct 11 15:12:08 2013 -0700

    Merge branch 'master' into commprof

commit e338a51ce401786d58f2c1c071add58d0238a9cb
Author: vince <vebeckner@lbl.gov>
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 6a51cba9a2e537c35ff30c879818ec85ba7bdb81
Merge: ab740a0 46d89ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 9 13:28:05 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ab740a0e18d37276043a1413297e62cc24c51ce6
Author: lijewski <mjlijewski@lbl.gov>
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 46d89ca3400bdf46501df2b7a8fd672546de08c1
Merge: c897aab b8cc570
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Oct 9 10:33:45 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c897aabf5431930dcbffd0a6d39d90d4debc6a26
Author: Matthew Emmett <mwemmett@lbl.gov>
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 b8cc570a6c6302ee92e6bd50b5744b09c7ad45da
Author: Ann Almgren <asalmgren@lbl.gov>
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 311e94e3e8fee28387d661b1227c249f038904c6
Author: Ann Almgren <asalmgren@lbl.gov>
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 dc1e35566d731727ee57c01f5d1851affb300c91
Author: Ann Almgren <asalmgren@lbl.gov>
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 f128d84bd70ef5a4f31ec66220a59455b4dc7c3c
Merge: 18a498e 0eed263
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Mon Oct 7 19:23:39 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 18a498ebff72e85ff2f76538a45573f7c4e22f5a
Author: Michael Zingale <zingale@localhost.localdomain>
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 0eed263fd45c0a3a31b2a12f830192ea671f2c34
Merge: 0bed6d2 89e87bb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 7 16:21:42 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0bed6d2ef1df803b1da469596f42bd1f99ec6718
Author: lijewski <mjlijewski@lbl.gov>
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 89e87bb77edb41881a59dfbece896d1d7feb0e12
Author: Ann Almgren <asalmgren@lbl.gov>
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 a7aa21b7e769e4c8e0b5365c11b3d5e5dc426b53
Author: Ann Almgren <asalmgren@lbl.gov>
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 06782ac54efebee4be74ad85f408011ea7662c67
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 7 13:28:06 2013 -0700

    Inputs for nodal dense stencil test.

Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense

commit 2ab88b31b48d7b6a802db21406b37df17c260fbf
Author: Michael Zingale <zingale@localhost.localdomain>
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 1c957c006aa73a3dd647f95a928259bc13a270f0
Author: Ann Almgren <asalmgren@lbl.gov>
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 580e8f0e4ff97d4e90ebe44f012301174f5f1780
Author: lijewski <mjlijewski@lbl.gov>
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 ef4db703005dede233fa29317026883245f282d4
Author: lijewski <mjlijewski@lbl.gov>
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 f591bcb40b690fbfb021dd37a6ea83bc5530aae6
Merge: a90db69 963787a
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 2 20:41:06 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a90db692965b4c44e1f855e5f69c8c9611bdc877
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 2 20:40:42 2013 -0400

    add default values in [] in the print routine

Tools/F_scripts/write_probin.py

commit 963787a8f3cc03de96479dfc5c12bce30f8d04ef
Author: lijewski <mjlijewski@lbl.gov>
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 45127e686244c3be51362c11383e746c8ee02e73
Author: lijewski <mjlijewski@lbl.gov>
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 b9c8291683e16118854bd2e5539d068bbab2727c
Author: lijewski <mjlijewski@lbl.gov>
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 e5abf55139fbdc44940de32b582108afcbd1081b
Author: lijewski <mjlijewski@lbl.gov>
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 0d8dcab43a244e53d1e3465d2e996d841fcda657
Author: lijewski <mjlijewski@lbl.gov>
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 4ec0ae0d1f38b9c44f8d4f5be8f294bd9e15dcbe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Oct 1 16:27:45 2013 -0700

    More work on double -> float conversion.

Src/C_AMRLib/Particles.H

commit 5fedf8834306e0d4807044f9b4dc96ba2d55be62
Author: lijewski <mjlijewski@lbl.gov>
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 8125a578b873356c8ce6e1c2d627582323f1265e
Author: Ann Almgren <asalmgren@lbl.gov>
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 bea6d1b2afdfa912678c183aa887991423f8be6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Oct 1 11:12:40 2013 -0700

    Add ParticleBoxArray option for AdvectWithUmac.

Src/C_AMRLib/Particles.H

commit 1163d71b3e5ad8be744d3c596b96a0e7a2ee7d2e
Author: Ann Almgren <asalmgren@lbl.gov>
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 909155c1bf1310f4b0957e8f1de5ba243e5ce5b5
Author: Ann Almgren <asalmgren@lbl.gov>
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 a0fa1d54b0777de9e759b3000b2b87e61be2742c
Author: Ann Almgren <asalmgren@lbl.gov>
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 960eea93241a5984459755719b55bf24ccea4f2f
Merge: a608705 5530bdc
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 30 12:44:53 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a60870593db1eea3e11a8763fb3f73a52c8e2efb
Author: Ann Almgren <asalmgren@lbl.gov>
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 5530bdcd66511988e5015fa55d8004744a11ce09
Author: Matthew Emmett <mwemmett@lbl.gov>
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 0cdc484807a6a966ddb0183bf996cb9c833a5221
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Mon Sep 30 09:54:45 2013 -0700

    Add setMidData.

Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateData.cpp

commit 510ce4f26db37b0c1c34bc7e9ed92de15db8949d
Author: Ann Almgren <asalmgren@lbl.gov>
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 b515c42bd789d195418c6222d9dbaad8ce2be5c3
Author: Ann Almgren <asalmgren@lbl.gov>
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 6956653e20a132b9875ab50327657b8f27749ae1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 10a12b95e3bc67b8a2fbb0c456268dec5f957929
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 27 11:07:09 2013 -0700

    5th-order interpolation in 3D

Src/C_AMRLib/INTERP_3D.F

commit bd924155e060233fc7f01f70191da13d7941a0ba
Merge: 45ed898 6f553ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 27 08:23:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 45ed89856243a7c4d1b2d2a780b241499d107daa
Author: Ann Almgren <asalmgren@lbl.gov>
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 6f553ef1251fa6eec5eb042ab296e61219af5abb
Merge: 5fad865 ef1d54d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Sep 26 22:17:42 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5fad865f27d9a529c14bc186982787e0d8b3c5fb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ef1d54d738f858a4fcae202a3b2939c03c2634fa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:54:03 2013 -0700

    Little more tweaking of output in InitFromBinaryMetaFile()

Src/C_AMRLib/Particles.H

commit 7fe18fd2a893352be67d5ef062209cb299d24411
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:41:53 2013 -0700

    Added some verbosity.

Src/C_AMRLib/Particles.H

commit ff0b75eaeccf344416430f0401363e1739ff9a62
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 26 15:38:42 2013 -0700

    Added InitFromBinaryMetaFile().

Src/C_AMRLib/Particles.H

commit 178971219322ecb5bf6843601c45ac6498878599
Author: Ann Almgren <asalmgren@lbl.gov>
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 1f50252d92bb476dc94ab258ccb1ef1544b58904
Author: vince <vebeckner@lbl.gov>
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 6e19668c2b5aa84b636da059be3642feddb96065
Author: Ann Almgren <asalmgren@lbl.gov>
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 8a0c50868aca28827ff8a30f83dda7b16a69cd06
Author: Ann Almgren <asalmgren@lbl.gov>
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 160a59122b0cc8ed57f55756de8e4e9ca2c6c107
Merge: 7620ebd ce172ca
Author: vince <vebeckner@lbl.gov>
Date:   Tue Sep 24 12:44:58 2013 -0700

    Merge branch 'master' into commprof

commit ce172ca1dc64a418ff43be452caa20c9041db699
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Sep 24 10:07:54 2013 -0400

    update Maestro tests

Tools/RegressionTesting/Maestro-tests.ini

commit e44fc2d85f4f2e1649c7dff2eafe0cd5cec6ce1b
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Sep 20 13:50:00 2013 -0400

    fix globalAddToExecString

Tools/RegressionTesting/testnew.py

commit 561bdd52c3b7d80459e940824327d632967ab7ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 20 09:29:40 2013 -0700

    Remove GETPLANE.

Src/F_BaseLib/fabio_c.c

commit f0dd557d629be2e4b01c3cd1882f086255c46236
Merge: a91c8dc 015a2fb
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 20:06:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a91c8dc7d5ca6d330f8e946611232872d0ab151b
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 20:05:46 2013 -0700

    fixed bug in check of uniform mesh

Src/LinearSolvers/F_MG/mg.f90

commit 015a2fba1c734b6b2a7a17ab90ff41d83431d4b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0d0d4974991c37a5cedb8fefb8603bc6f5206a0d
Merge: b72cb6d 4a85945
Author: jbb <jbbell@lbl.gov>
Date:   Thu Sep 19 10:47:34 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4a8594538cb83dd4a7d12a7a983d5bf1c8465077
Merge: d6de81d 5edabd6
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 18 17:30:09 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d6de81dc3f077ca340270a0686feadb052b6798d
Author: Marc Day <MSDay@lbl.gov>
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 5edabd6327d9e6935e6b36ecfcc1e998b6efbdfb
Merge: 2c71109 909e626
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 18 15:58:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2c71109831c55a590a5233a3b228ef75e7b1d1bb
Author: Ann Almgren <asalmgren@lbl.gov>
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 909e626c7c29a19858a9d7fbcc86e16d0c6f516f
Merge: 5e578b8 fc2c77a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 18 15:20:30 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5e578b8e1fda27cf8f3c4ae36c302cc6f0383e66
Author: lijewski <mjlijewski@lbl.gov>
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 fc2c77a18a90a9d2c67a3aa901116be7f4121d96
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 18 12:49:45 2013 -0700

    up the tagged version num

Tools/CMake/BoxLib_Version.cmake

commit 6356be7e1aee8da83fbb9e102f8141d74f685e9d
Author: lijewski <mjlijewski@lbl.gov>
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 e6983ab620c7cf0f6b84e18a311ddef92bcdafa7
Author: Marc Day <MSDay@lbl.gov>
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 35ae2af53a127c38ee3dafd2af74bc24319cace1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 606e47f3014797e07381ef3653c817283249b560
Merge: 99b38e8 1674226
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 13 11:43:29 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 99b38e8691bab67c721c17c29b24f27f1da03102
Author: Ann Almgren <asalmgren@lbl.gov>
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 1674226c0b6735cf5812f0274c21da18ac7d8788
Author: lijewski <mjlijewski@lbl.gov>
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 8ccd5122cde53b9f9746ce15a30b51a6d0adf9c2
Merge: 5cbc021 539beb0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 16:00:13 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5cbc021fb69d8a7bb72b8ec294dfad5c1b78ccef
Author: Ann Almgren <asalmgren@lbl.gov>
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 7620ebd70757f693076524e1ffbf8b1b5dbb95f4
Author: vince <vebeckner@lbl.gov>
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 539beb0553474dd37152cc3fbccb0eb121062123
Author: Marc Day <MSDay@lbl.gov>
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 2819e118b9213e145d4458d8f8fe044e6d7191a4
Merge: 306eeab da42599
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 12 12:16:53 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 306eeab744ccfb682c9d97fa57928f964f2d61a1
Author: Marc Day <MSDay@lbl.gov>
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 da425996113626004b842ab61abc18a58c054971
Author: Ann Almgren <asalmgren@lbl.gov>
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 84a2455ab00e992d8222bb6ab17e4f95a0355555
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 12 10:02:25 2013 -0700

    Add domain vs lev0_grids check in defBaseLevel.

Src/C_AMRLib/Amr.cpp

commit 62c7a46373a9a5a1ddb7a074144f799356789101
Author: lijewski <mjlijewski@lbl.gov>
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 afa55bf51837e28b4154bb9acd9df8ac5b51fdba
Merge: a112aaf fb587de
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 11 17:19:32 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a112aaf3bf0d43e5c9199ccb485739a01213d25f
Author: Ann Almgren <asalmgren@lbl.gov>
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 fb587de91f0305b46f04f15c9f9a0f7a013fa5cb
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 16:48:49 2013 -0700

    Update version file

Tools/CMake/BoxLib_Version.cmake

commit 38f460235ae7027382fc1c1c7bcb20eae98fb93c
Author: Marc Day <MSDay@lbl.gov>
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 475251acb7d1edf6e370ea37068e64209a90ec30
Merge: 21fc642 c56e365
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 15:52:21 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 21fc6426ecb030417fb4eb80d3d6c238e1c23f3e
Author: Marc Day <MSDay@lbl.gov>
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 c56e365642ee7f6c9d09ee957372581cdcc60835
Merge: 1d0a665 1359043
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 11 15:18:35 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1d0a6654f4211fc7da42cc5031b30043e3087184
Author: lijewski <mjlijewski@lbl.gov>
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 1359043843dce946759141ebfa1edf9e5eca2317
Author: Ann Almgren <asalmgren@lbl.gov>
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 68028afe93d2661616c625a435a4e1dd605071a4
Author: Ann Almgren <asalmgren@lbl.gov>
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 97aaa120bb070f4f268013a0d18bf35529ac2295
Author: Marc Day <MSDay@lbl.gov>
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 7ed7f6d13d762e96d33ad0bf11cf34301b19ac17
Author: Marc Day <MSDay@lbl.gov>
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 5f6c46c13c1f84ccc13ad15f655bec1a29a8c1e5
Author: Marc Day <MSDay@lbl.gov>
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 31a715c322a21bdfad93641bcd8ad3273b576bd5
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 11 01:18:03 2013 -0700

    CMake install the mod files

Src/CMakeLists.txt

commit f303baa3773e7d1e90d6c8d8d36b56ffbe06b2fb
Author: Marc Day <MSDay@lbl.gov>
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 241eed3c92d40f9052f2c957952d14707f16602e
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 23:56:02 2013 -0700

    Add buildInfo.H to install

CMakeLists.txt

commit f4c238be632bd1ad105f5f1c019d0fe6cdb43f6a
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 18:47:50 2013 -0700

    Add Particles.cpp and Particles.H to CMakeLists

Src/C_AMRLib/CMakeLists.txt

commit bd7569a05e174a5b88f8ce584491f4192629f6f8
Author: Marc Day <MSDay@lbl.gov>
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 0c26d27df85b83df2fc1f4da90db4dd22f608240
Merge: 3f8312d 77cba40
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Sep 10 15:31:01 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 77cba407956bb3bea68db004745a6b2260ce4de3
Merge: 6e0d0e4 7cc961d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 10 14:57:12 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6e0d0e484fb8c588a87aeb923f75d0c07f35fd56
Author: lijewski <mjlijewski@lbl.gov>
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 3f8312d593f6f2d7fde71d65f01875c2a4a15049
Author: Marc Day <MSDay@lbl.gov>
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 7cc961dc4cf66990ae6d40c8eb4d3417c5255e2b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 10 13:23:33 2013 -0700

    Add comment about RHS and SOLN and visualizing these.

Tutorials/AMR_Trilinos_C/README

commit d8363ad054587ef86fb3e773e9f0e10580102d7b
Merge: 86de1b5 03edb7e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 10 13:21:11 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 86de1b584f8669d809bb03186b3a2aa3a9615e11
Author: Ann Almgren <asalmgren@lbl.gov>
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 03edb7ee3773370acda82c00e6850a6c812378a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 10 12:23:01 2013 -0700

    merged 2 MPI_Bcast into 1

Src/C_AMRLib/Amr.cpp

commit b9852e8364bf85f4464ce21712929157ab835c5c
Author: Marc Day <MSDay@lbl.gov>
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 ab918220b0a4d390138da6aaad4dafb2f09850a2
Author: Marc Day <MSDay@lbl.gov>
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 166c8382f11b631022b6849042707538a46ce778.

Src/LinearSolvers/C_CellMG/CGSolver.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Tools/CMake/PreprocessBoxLibFortran.cmake

commit 166c8382f11b631022b6849042707538a46ce778
Author: Marc Day <MSDay@lbl.gov>
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 86c069116cef65d1e62b4fdec82869aeedbfe17c
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Fri Sep 6 13:01:41 2013 -0400

    find the / detection

fextract.f90

commit a98683be907c9a16c2029f07d0a868aabc2ad615
Author: lijewski <mjlijewski@lbl.gov>
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 ddd46eb0f139a0d031830b1e76cd00049c1f90a6
Author: vince <vebeckner@lbl.gov>
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 e24505cd767723b8e53221c8acc55fdbaad27e5b
Author: Ann Almgren <asalmgren@lbl.gov>
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 db44236d373e59edbf86d584cd3584829342ff19
Author: lijewski <mjlijewski@lbl.gov>
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 a6f9fa646c2c5fe5f6f77e0b93fb5091256c3676
Merge: 6b11003 d275a97
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Aug 29 00:45:08 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6b11003d5012ead43d674fc26ff714e1da7237ba
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 28 20:02:16 2013 -0700

    more minor mucking with cmake

Src/LinearSolvers/C_TensorMG/CMakeLists.txt

commit 7d6794f32a14273f2e8ab230a2a9cd06d67df474
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 28 19:45:37 2013 -0700

    minor mucking with cmake

Src/CMakeLists.txt
Src/LinearSolvers/C_TensorMG/CMakeLists.txt

commit d275a97708b4293d8edd0a266b403e0b4ac84c8b
Author: lijewski <mjlijewski@lbl.gov>
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 3eef9dafa3916a93da61cad716076f8ef0ccf0cc
Author: lijewski <mjlijewski@lbl.gov>
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 f8ae99aea130b17aae47e80edef4b5a4d45ea51e
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Aug 26 20:58:48 2013 -0700

    Moved function into MCLO_3D.F

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 70d9eb64b1827b8517fc1f29ca8ba65b7585ff6c
Author: Marc Day <MSDay@lbl.gov>
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 863edc4a58441ae86b88a8a0f72381b608727d69
Author: vince <vebeckner@lbl.gov>
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 f907ca8fdc57d450cd16ac32681cfebcdd734737
Author: Michael Zingale <zingale@localhost.localdomain>
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 60267c24ab1d29c60e54ad0a1ca6e7142cbedaad
Author: Michael Zingale <zingale@localhost.localdomain>
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 6d4080c8abfaea70a15d86fe28beda9e70c67a2d
Author: vince <vebeckner@lbl.gov>
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 0cf361a0756e63a2f997e4f50bab4db0067c8250
Author: vince <vebeckner@lbl.gov>
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 6bf5969d2940fdf987135d58601d8b921066e2b5
Merge: 44eb148 88bde8d
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 22 12:41:25 2013 -0700

    Merge branch 'master' into commprof

commit 88bde8dd85518effb256312164ada78daf47cebc
Author: Matthew Emmett <mwemmett@lbl.gov>
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 44eb1480b0be84cf5716892ec38b374afee8c8f7
Author: vince <vebeckner@lbl.gov>
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 93cfaaa2f0eaccfa2a6e8849283d9b92f9a4ac89
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Fri Aug 16 10:38:43 2013 -0700

    Changed REaDME

Tutorials/MultiGrid_F/README

commit f8b7e88e65ba05f8034eb8003b4fcca9f7518ef3
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
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 325ff3aa1217cf2fe680ca702cd99021e2ee110b
Author: vince <vebeckner@lbl.gov>
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 e27d900962fef19943c481ff960e04c97e905a1f
Merge: 78bafd9 d732127
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 13:16:58 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 78bafd9dc40a56a8c4a2e32ab3b8ad5c881073cd
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
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
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe

commit d732127f9df80edb26d0bb7ac43cf9c910d9590d
Author: Ann Almgren <asalmgren@lbl.gov>
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 f9638da29b903dab35c923827ebe597c73cb3ae1
Author: Ann Almgren <asalmgren@lbl.gov>
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
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe

commit c1e78af163733b10a873c6cd0f3e178c298e0345
Merge: 6641ec7 dd9f030
Author: Jonathan Wang <jmwang214@atragon.lbl.gov>
Date:   Thu Aug 15 11:03:39 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6641ec7d06c2fe6c1228510c463a470838700b54
Author: Ann Almgren <jmwang214@atragon.lbl.gov>
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
Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe
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 dd9f03060efcca337a064ccce2d36dde2da66a7c
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:52:40 2013 -0700

    and an mpilib....

Tools/F_mk/GMakeMPI.mak

commit b8970d804517aa12a5141ea074631541bfb51f75
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:48:54 2013 -0700

    and for fortran.

Tools/F_mk/GMakeMPI.mak

commit b2c1d2e3e354588baa82518c54473f3c99c9cdfb
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 14 09:45:00 2013 -0700

    fix for gigan.

Tools/C_mk/Make.mpi

commit 47abfaa1a89f7debdd3f2b6284929e9c60e2136a
Merge: 3802df5 001a103
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 8 15:06:42 2013 -0700

    Merge branch 'master' into commprof

commit 3802df5d9356b62986d032345c08d6c3c6eb4b6e
Author: vince <vebeckner@lbl.gov>
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 001a1039aa97bc1af99d668a282812d88d6aaa8b
Author: lijewski <mjlijewski@lbl.gov>
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 e5cff7835f97d7675652cd528ba910634bdd96d5
Author: lijewski <mjlijewski@lbl.gov>
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 cea0fab7ebac08b7cf9782036bfc13951a9e6c37
Author: lijewski <mjlijewski@lbl.gov>
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 bb474d0505c9746cbd7cacbe3e08202a2e439bcd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 6 13:42:48 2013 -0700

    Added qdotxy().

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8902719bb281aba84ae1ea0ccb7c7c6afc0abdd1
Author: lijewski <mjlijewski@lbl.gov>
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 7c801bba2b708e95d770ad058e4f48e1bf2f4ace
Author: lijewski <mjlijewski@lbl.gov>
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 660b1a179ea51a0e53a6b17756cd1ea9b65366f3
Author: lijewski <mjlijewski@lbl.gov>
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 63d775ddcc7d6d0d0af135ef0885ec0860ca3d88
Author: lijewski <mjlijewski@lbl.gov>
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 217c63b93f4a0461be7d9c3d6d3b9a4810ae67a2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 5 11:41:15 2013 -0700

    Just a little code rearrangement.

Src/LinearSolvers/F_MG/mg.f90

commit 40ef685b98f9a1d61c418c09ef5b715fabf5796b
Author: lijewski <mjlijewski@lbl.gov>
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 642fe94b6358ba86c20ef1dd8246cbd3f4d3e4b7
Author: lijewski <mjlijewski@lbl.gov>
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 52f0bd84d605a9080d90b8370e7d1c4461b60706
Author: lijewski <mjlijewski@lbl.gov>
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 1a6bade001e25aa1708d60f762ed64db4707e72a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 1 14:08:32 2013 -0700

    Some work on edges & corners for 3D lininterp.

Src/LinearSolvers/F_MG/mg.f90

commit 28c5715e8e88ac7348dd65feb866eddedf032eeb
Author: lijewski <mjlijewski@lbl.gov>
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 3c2a83aa55f16b06b22681151d6a8b437b5a5b1e
Author: lijewski <mjlijewski@lbl.gov>
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 356ca7291d3bb37899968c7c4666270742fc1ad2
Author: lijewski <mjlijewski@lbl.gov>
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 f375ef92a90a6725095e129ceb2904c209c4bb3d
Author: lijewski <mjlijewski@lbl.gov>
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 419e49501d44edd18c07de271924bdfbbdd36258
Author: lijewski <mjlijewski@lbl.gov>
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 04836f40290547005b4cee45cef1ad32f107420b
Author: lijewski <mjlijewski@lbl.gov>
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 4cbc69a5d903430c161a926ea05258effd03e809
Author: lijewski <mjlijewski@lbl.gov>
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 e0e55541b4972e41817df08acb20e51087d330ba
Author: lijewski <mjlijewski@lbl.gov>
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 2aacddc05d75929b9c208db24f7ce072c68d3fd5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 16:56:16 2013 -0700

    A little cleanup.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit feccdf0061edcc1f59433cdb783eefe8d0533e14
Author: lijewski <mjlijewski@lbl.gov>
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 e983a7c7a430692610b463214001c0c42cf408d3
Author: lijewski <mjlijewski@lbl.gov>
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 953784b78df701e9cfef981e9896711e7b4a9d3e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 14:55:45 2013 -0700

    Bug fix.

Src/LinearSolvers/F_MG/mg.f90

commit b9b2bd8c0c93cecacca4da03602ed9524e044f24
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 30 13:45:54 2013 -0700

    Added some commented out debugging code.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 41e6de9662db42c11ae776b98f9c5ae11d194fef
Author: lijewski <mjlijewski@lbl.gov>
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 2bbc0be66ca6424e629c3bcc1e7b4bc1a4f383a6
Author: lijewski <mjlijewski@lbl.gov>
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 e00a6e5a1b5f89a3c7bcdb597f46ac822e1fe4b9
Author: lijewski <mjlijewski@lbl.gov>
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 23ccee4f498606ae2750fa336ead802bbeae2ee3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 15:34:38 2013 -0700

    Added some debugging code.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 64b85dc81f5153c98cf18c77e06a1285513b59d3
Author: lijewski <mjlijewski@lbl.gov>
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 a12f017a97228aceee6191dce8a59c0542f72dcd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 15:33:12 2013 -0700

    Print out cycle_type when outputting settngs.

Src/LinearSolvers/F_MG/mg.f90

commit 2f1914ddf8d60127ee8e954fbb06c4624c67f788
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 29 12:29:39 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit 160ce7630e9ed22534afc9fa694bfe881351f643
Author: lijewski <mjlijewski@lbl.gov>
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 78b2d5fbfbee2fc2bca5a3028075c1dcff3d6f3b
Author: lijewski <mjlijewski@lbl.gov>
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 8c091e47affba52a9c5d6a6a6f1a5cc010181b8c
Author: lijewski <mjlijewski@lbl.gov>
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 a68873b39bb0af2c718b56ba46530dc051306463
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 16:10:30 2013 -0700

    More prep work for tricubic.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit fc6e12ecb5e199cb95b509998563405d55423e0e
Author: lijewski <mjlijewski@lbl.gov>
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 75702a7541f24f755e4115969253902597c24399
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 15:25:39 2013 -0700

    Removed some divides.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit d4bab1cac66356d34af9ef1b15e093790c924e52
Author: lijewski <mjlijewski@lbl.gov>
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 f3d783c3586d27639394aab28f93dcbee67de014
Merge: b744b6e a943022
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 26 14:22:54 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b744b6e4855e9786c2c9457857b53ebc109830ed
Author: lijewski <mjlijewski@lbl.gov>
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 724ed423e488dea769f958102ebc3fa1e6d16e48
Author: lijewski <mjlijewski@lbl.gov>
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 a94302267f7b938d838c86b55da424501907d062
Author: vince <vince@gimantis.lbl.gov>
Date:   Fri Jul 26 10:32:03 2013 -0700

    fix for intel on gimantis.

Tools/C_mk/Make.defs

commit 7ae3cd77a78540b40df143185ed2d17b84a0d650
Merge: 840d2a3 f6f6c84
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 25 15:28:11 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 840d2a32558d6cd4ef41a47f513414cb86d50c71
Author: lijewski <mjlijewski@lbl.gov>
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 65aaac7538828bb7cf2bb25cd80f39a15ba833c6
Author: lijewski <mjlijewski@lbl.gov>
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 401eda9502f1de648431912be354dab40aa3e3da
Author: lijewski <mjlijewski@lbl.gov>
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 4c54023e4896d174c0ccb6214909c8d6b48ddde2
Author: lijewski <mjlijewski@lbl.gov>
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 86dbe528fcb27e47da213d1d5e51cd0d4b1dc940
Author: lijewski <mjlijewski@lbl.gov>
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 f6f6c84784ce1a689f49794faaebc648489dd9a7
Author: Matthew Emmett <mwemmett@lbl.gov>
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 0299238ac61b3a90a8697c9ac2fc083ebbea8097
Author: lijewski <mjlijewski@lbl.gov>
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 d72fb9a56e39ab01764d4b69c9a3a74de80bfa1c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 16:47:26 2013 -0700

    Implemented classic #D full-weighting restriction.

Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 489a3fcbe1cd223900704727c45b43dcb9fc50c2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 24 16:47:04 2013 -0700

    Removed those HACK multiplies after restrictions.

Src/LinearSolvers/F_MG/mg.f90

commit 2dc8149a5dcc6a2c4d2ac4cbd4255e9200f72c45
Author: lijewski <mjlijewski@lbl.gov>
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 506cab010d867a39bf1f91ac3db2ce8b63fcc812
Author: lijewski <mjlijewski@lbl.gov>
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 915646ec0e3eb5fa9169753f6d44b4bb20433187
Author: lijewski <mjlijewski@lbl.gov>
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 47653736a4981ac3630380db8682571e7469bcac
Author: lijewski <mjlijewski@lbl.gov>
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 3cb03c89af502ec4b81528d2c6b25512dc459b6b
Author: lijewski <mjlijewski@lbl.gov>
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 873f7deb196ef9048796f42ed14b264dafb82772
Author: lijewski <mjlijewski@lbl.gov>
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 bd4cfdf73943dacd461f86f3c2fea82095fec88f
Author: lijewski <mjlijewski@lbl.gov>
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 1edf4598b5ddb57786e8ea8faa04557412c8474d
Author: lijewski <mjlijewski@lbl.gov>
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 82cb27d311357074e6fd701ed1b2d119388dd040
Author: vince <vebeckner@lbl.gov>
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 0084aea3a2ff27744f6a6f1d5d9a6b92bc5024bd
Merge: d94495a 12633de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 23 10:05:46 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 12633de0560fdf0ab0894c83c19e5ceacfa658d7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 22 12:37:15 2013 -0700

    Add new file cc_edge_coeffs.f90

Tests/LinearSolvers/F_MG/GNUmakefile

commit 438616f07fbc74cd0043b6a419d001221796e36a
Author: Ann Almgren <asalmgren@lbl.gov>
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 896a0273cdb0d567c062413f2cc969b2593d957b
Author: Michael Zingale <zingale@localhost.localdomain>
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 8c7d5d3a1d5832789edd7ce43cc285e923c4e1cc
Author: Ann Almgren <asalmgren@lbl.gov>
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 477b7222a90013c423ff12fd0483bd3b71cb384f
Author: Ann Almgren <asalmgren@lbl.gov>
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 d94495a7a198624a9149331041e58b1fcd39d5b1
Author: lijewski <mjlijewski@lbl.gov>
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 cb151fc25dd0b92e0fbd1222974141700146b215
Author: lijewski <mjlijewski@lbl.gov>
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 882d3755ee061ec0033f1f01c1387cc587130848
Author: lijewski <mjlijewski@lbl.gov>
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 9009890e22bf1dc38e22f70710436d12daa28d9f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 14:52:44 2013 -0700

    Little more cleanup.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit f248f79ab22d8a4092e1d504de30ac5b55af183c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 13:45:05 2013 -0700

    Some cleanup of new linear prolongation operators.

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit bbfeb862ef57dd3c5df7e65253d002ad9764ebbc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 19 12:04:18 2013 -0700

    Removed unnecessary fill_bounary() in special bottom solver.

Src/LinearSolvers/F_MG/mg.f90

commit ea9200968c41e8ea6061971a8598d1e5a072af05
Author: lijewski <mjlijewski@lbl.gov>
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 e6c99fceaf50545b32aa9b9a1afe35ae19ddd078
Merge: 7fe3c4c a5a4705
Author: Ann Almgren <jmwang214@atragon.lbl.gov>
Date:   Fri Jul 19 10:45:51 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7fe3c4c1843a797c47a4d34e53796cfe9d3bff62
Author: jmwang214 <jmwang214@atragon.lbl.gov>
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 a5a470571ef9b200095f35666030b58abaabf462
Author: lijewski <mjlijewski@lbl.gov>
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 321516692171b1020e78fb4ae346466019cb70f1
Author: lijewski <mjlijewski@lbl.gov>
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 b7dd2b75e3b787fddaa347b8a9f17a1607bbc753
Author: Ann Almgren <asalmgren@lbl.gov>
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 b1a802a8df6ed5cb552abf7566e9e130e18e9418
Author: Ann Almgren <asalmgren@lbl.gov>
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 fac7171aa1cf6c04870dc1f82857e80abc9fd59e
Author: Ann Almgren <asalmgren@lbl.gov>
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 f47a0731728f2512b2adee9a2a668a9a2fb505cb
Author: Ann Almgren <asalmgren@lbl.gov>
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/inputs.simple
Tests/LinearSolvers/F_MG/inputs.simple.3d
Tests/LinearSolvers/F_MG/test_script
Tests/LinearSolvers/F_MG/wrapper.f90

commit 9ac40b68057b4dc5c184460219696a86fe04ffb0
Author: Ann Almgren <asalmgren@lbl.gov>
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 19576081fb0b3b462ec7d0516b1a1fee1d0350ba
Merge: aeb2773 7bf6bfd
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Jul 17 08:59:10 2013 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit aeb27732487ce6e0b639e3c2fe00b476d1c7fb28
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Jul 17 08:54:11 2013 -0400

    add FIVE3RD

Src/F_BaseLib/bl_constants.f90

commit 7bf6bfd4937afeff9c6350f5d314e7be69c760fa
Author: lijewski <mjlijewski@lbl.gov>
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 182afceec7ef80b8a1893383889db2c569a90f90
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jul 16 10:06:28 2013 -0700

    omega is no longer part of mg_tower

Tutorials/HeatEquation_EX5_F/advance.f90

commit 93bb923fe7843c8c67fb9b374a74ccc0938f83d5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 15 15:32:49 2013 -0700

    Add timer stuff to f_cycle.

Src/LinearSolvers/F_MG/mg.f90

commit 0577a802d2c8aaa11d34b0023f8f700b9ecdb891
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 15 15:30:57 2013 -0700

    Remove unused nodal_flag in fmg_cycle.

Src/LinearSolvers/F_MG/mg.f90

commit 4809d1651451e34268f188404b82b2e731967a77
Author: lijewski <mjlijewski@lbl.gov>
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 7a76e3b900ba28ef7c8efc6204a9515e553d7a88
Author: lijewski <mjlijewski@lbl.gov>
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 fcc9754c0ec3eabbbdafe771c465961e591437d3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 13:43:20 2013 -0700

    Only set mgt%face_type if nodal.

Src/LinearSolvers/F_MG/mg.f90

commit 4e2afe6241778a3798fa6bddab6bc4e67e52e67f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 13:22:28 2013 -0700

    Skewed stuff.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 56ab461ce41bec8900a22b381898b3bf7489d3d9
Author: lijewski <mjlijewski@lbl.gov>
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 f4fb330d250e2a804a768838e666e608e94fe402
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 12:11:56 2013 -0700

    Do error check for cycle_type.

Src/LinearSolvers/F_MG/mg.f90

commit 4c3cb56dd2ba6fbbb31178b4350eb404c39b3fe6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 15 12:11:37 2013 -0700

    Added --cycle_type.

Tests/LinearSolvers/F_MG/wrapper.f90

commit c73e1db6ec693d5b7351584a0b813908a9696476
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 15 11:41:51 2013 -0700

    spacing.

Src/C_BaseLib/Profiler.cpp

commit a6f3fd4ca01b5293fc800942487f53ca263e49c5
Author: vince <vebeckner@lbl.gov>
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 32f9d6a1025bb8c0df88d63de7eafe33fead5d24
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4d3be1fe98f254628b1f5d1ee7ca159096074d97
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jul 10 13:36:43 2013 -0700

    comments for mg_max_levels function

Src/LinearSolvers/F_MG/mg.f90

commit f293f2d9cad5107f7249a660923a4f9880aea0f7
Author: Ann Almgren <asalmgren@lbl.gov>
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 c133947bec199294415a2c905452105be9c3e9f1
Author: jmwang214 <jmwang214@atragon.lbl.gov>
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 b277c404726e2f0c06027c10c43a4eb5036715a6
Author: vince <vebeckner@lbl.gov>
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 44c75a7536ca029cd41466306abd78fbe0914805
Author: Ann Almgren <asalmgren@lbl.gov>
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 3c690665131fe0da8adabe32b7446ea6df398a6c
Author: Ann Almgren <asalmgren@lbl.gov>
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 5d4cea36189bf7b14b9b01626fdb78b2c3b44d85
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 8 15:52:40 2013 -0700

    Declare mgt%visited.

Src/LinearSolvers/F_MG/mg_tower.f90

commit b7381559b2455abb2c0b590d99ed3acb5f698a51
Author: Ann Almgren <asalmgren@lbl.gov>
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 53e05eb7d845a5983cd0f100171608d46f10b0c2
Merge: 58b5bbb a8aed60
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jul 8 13:34:06 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a8aed6002f7d9cd9e0c5b2981239c5b26d579c86
Author: lijewski <mjlijewski@lbl.gov>
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 4ccdeca95ee2ffcb0fe35c96239da028a979652b
Author: lijewski <mjlijewski@lbl.gov>
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 58b5bbb3c209be2016fa1a7f31198d60cd5ff887
Author: Ann Almgren <asalmgren@lbl.gov>
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 b105800b6e9f28843d849f1632ca0493598ebac9
Merge: 2a613f6 714551b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Jul 6 09:27:49 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 714551bbb19c3946b792d1b46924147dcd55da09
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 2a613f62b3d3a237aa36aca5c6968d92b40ced15
Merge: 4932bec 8da5f10
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 2 14:54:21 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8da5f10a310649677b12a0dd77683e616d19e8cb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 2 13:45:57 2013 -0700

    Add WritePlotFile in Particles.H

Src/C_AMRLib/Particles.H

commit 4932bece7152507e5e54ea85bf63eb104f5f2b3c
Merge: 786d24e a16bbc7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 2 11:05:40 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a16bbc76fde8b7e0db48f8fde9fa0431e0039f29
Author: ajnonaka <AJNonaka@lbl.gov>
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 786d24eb7626bfea3479e43d60e6cc92589cb5fe
Author: lijewski <mjlijewski@lbl.gov>
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 9de67f2fd397d0163ab6dc3cd15272061e6fd704
Author: lijewski <mjlijewski@lbl.gov>
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 de62800c3ea546a4da06eaa70b62a02edbb8bffa
Author: lijewski <mjlijewski@lbl.gov>
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 aa0608c319ef2b6ebae171fce81e6779fcb2c89a
Author: lijewski <mjlijewski@lbl.gov>
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 def0336d981e10866f54447b029754c3597e6cff
Merge: e1b9cb9 f278203
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jul 1 10:36:23 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e1b9cb938ea2f1a96288c3e9df8f20de72ddecd0
Author: ajnonaka <AJNonaka@lbl.gov>
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 f278203e7ef2f1a80bfa598bf2e846541154addd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 1 08:30:55 2013 -0700

    get around a PGI compiler bug

Src/F_BaseLib/multifab_f.f90

commit 9100a79ed4aed3574bce691727009ec53f1cc702
Author: ajnonaka <AJNonaka@lbl.gov>
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 b0d52a253a8b58eedfe11a9ddd9cc58413b57145
Author: ajnonaka <AJNonaka@lbl.gov>
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 738994822f85cb0dcee361580d5fc46836cdf73e
Author: ajnonaka <AJNonaka@lbl.gov>
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 4fbfd3c5d9f83e393285c2b7034e584743392740
Author: ajnonaka <AJNonaka@lbl.gov>
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 e2a1cdd8895424145a3d6383e346cfaa2dc3ff3d
Author: lijewski <mjlijewski@lbl.gov>
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 d91fcdc5e75876de1abced925830ba88f9ff4f2c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 26 11:08:28 2013 -0700

    Removed some trim() calls on string comparisons.

Tutorials/AMR_Advection_C/Source/network.f90

commit d32858a52e13f8e27ddab807fe838296a5673a01
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 26 08:11:33 2013 -0700

    Got another 20% out of fourth_order_interp_2d().

Src/F_BaseLib/interp.f90

commit 43b08071ee921a5e06670930cef462905d635c04
Merge: 11bf3db b0da2f9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 25 15:38:10 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b0da2f95ddb90c1188fb42a62617a0455337ccd6
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:52:15 2013 -0700

    added nametags.

Src/C_BoundaryLib/FabSet.cpp

commit 329d2bc9905a35be72fe3bf0fdccd5d5547f3e61
Author: vince <vebeckner@lbl.gov>
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 98bf4d3893cb08628ac81c95ac8403248e559834
Author: vince <vebeckner@lbl.gov>
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 d100d8d76f5fe89869c16d0d7837ac00ca30ee79
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jun 25 14:41:41 2013 -0700

    added to docs for comm profiling.

Docs/Readme.profiling

commit 11bf3db9077d315c21522758cdde511bafdca90c
Author: lijewski <mjlijewski@lbl.gov>
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 8dbbada1e1485f174f37697a5a54c4c71c98d952
Merge: 4357fcd dc0ceee
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 24 16:21:27 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4357fcd6226605580812d6b929f5d9f2ccf4ea42
Author: lijewski <mjlijewski@lbl.gov>
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 dc0ceee7a50d0cdd4317fce3c66fc735cef92fdd
Author: cmalone <malone@ucolick.org>
Date:   Mon Jun 24 18:06:45 2013 -0500

    cray compiler requires IO unit on flush

Src/F_BaseLib/parallel.f90

commit 657f90664e7c628d95f25fb0c9b29f4e4ce359ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 24 15:55:15 2013 -0700

    kind=8 -> kind=dp_t

Src/F_BaseLib/fourth_order_interp_coeffs.f90

commit 984a02cd79d56d0ab4722acda344b7e8d52ed7e1
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 c9bd3dedf14861b08472dedbd41492f670d0fb10
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cabcb2a1f5b2d5d6d3aefa27e440737e9bc7b5a6
Merge: db0d038 5bd0b35
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 21:45:48 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit db0d038517d34af15ab7dc864887dae8c1521c37
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Jun 23 15:17:48 2013 -0700

    fixed a minor memory issue

Tutorials/AMR_Advection_C/Source/ADR_setup.cpp

commit 5bd0b350c38192996223034f648fbed2ad717e4b
Merge: 7211c1e 13cb18a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 23 07:57:50 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7211c1ea01ab7a553630395f639ab6107c2e3d66
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Jun 23 07:57:30 2013 -0700

    Mod to parallel_create_communicator().

Src/F_BaseLib/parallel.f90

commit 13cb18a54e67b6228bde070d29885638b67c8e3b
Author: Ann Almgren <asalmgren@lbl.gov>
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 9caac1e5cbdc7d381adfdf9c6a0065a477341923
Author: lijewski <mjlijewski@lbl.gov>
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 c125c81a370729b4da569120c19d49eaa3a5ff19
Author: lijewski <mjlijewski@lbl.gov>
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 2a40dd3758401f99e6bc73dec9c0bba67627efed
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 15:26:06 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/mg.f90

commit d31115348b8105c22ab04ba98809ea8d7927d201
Author: lijewski <mjlijewski@lbl.gov>
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 38d682600d99c61530c869f4a57b0de04f654fab
Author: lijewski <mjlijewski@lbl.gov>
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 41f9a4f801f7d89f786a8a0f75772c21c8f30000
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 19 14:37:46 2013 -0700

    Used parallel_communicator() instead of MPI_COMM_WORLD.

Src/LinearSolvers/F_MG/mg.f90

commit a18a92091ee2d66c46d9f070028697b6d339acc9
Author: Matthew Emmett <mwemmett@lbl.gov>
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 ca7d98f3add60ebd535e9f5d60070b7fda0ec88d
Author: lijewski <mjlijewski@lbl.gov>
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 db02b8f90d988e49aabb928771ba72372e09c8a6
Author: Matthew Emmett <mwemmett@lbl.gov>
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 1154fa043f8db4e171703d00f8bf5bf5e2cc7c82
Author: lijewski <mjlijewski@lbl.gov>
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 14c178a96c506bebedbb4ead72eb2aa3eaf9633b
Author: lijewski <mjlijewski@lbl.gov>
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 72be4104ab91aa6fdc4b19dc3d7febce99662859
Author: lijewski <mjlijewski@lbl.gov>
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 36fca427106f7716d4cf08bfe2d17cb1869f77da
Author: lijewski <mjlijewski@lbl.gov>
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 12536f5634e27ea7f0acfbf189cbd830c52a13ea
Merge: bbdfe54 1602225
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Wed Jun 19 12:17:43 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bbdfe5459ade46aaec5b337311be5f4c7dcec814
Author: Matthew Emmett <mwemmett@lbl.gov>
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 1602225c5ee89a8207e65474094ed9936d2c3550
Author: Chris Malone <malone@ucolick.org>
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 1ab064adfad76bd92b0b04ed6bbe4a3e56d7ba92
Author: lijewski <mjlijewski@lbl.gov>
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 056d4bccf10e449afbb90eb35a4d75dc0c79f453
Author: lijewski <mjlijewski@lbl.gov>
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 ce0b32af4855b79f9822f0606a1bb4ca0f6faf58
Merge: 5ccb387 bfaea73
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 14:17:50 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5ccb3871e12a295cc2c424b64d8f7cacdab5c52d
Author: Ann Almgren <asalmgren@lbl.gov>
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 371fe1de14ab3e9b22d777ec923e5a7bbbd58ba7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 18 14:06:44 2013 -0700

    Updated which modules are included.

Tutorials/WaveEquation_F/main.f90

commit bfaea73b95780a3f3b81011485487d7a6c06130a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 16:26:03 2013 -0700

    Some mods to get it to compile again.

Tests/LinearSolvers/C_CellMG/main.cpp

commit 69b32fa6e6a83ffac38a4ed343636b242ecc79ad
Author: lijewski <mjlijewski@lbl.gov>
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 11d856e690ffb00c6ab82f09a5c0dd381156680a
Author: lijewski <mjlijewski@lbl.gov>
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 fe2ec96a6859a384567dc5a3c4cc4ffe585b48f6
Merge: a92f9ce 6c256b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 17 14:40:54 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a92f9ce7a6df22c1404ce9523cabdc07cfdba63f
Author: lijewski <mjlijewski@lbl.gov>
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 3574bba09a703acc872e6b6bf7c3eb14a76b6233
Author: lijewski <mjlijewski@lbl.gov>
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 3700fc70c407b6669925050f473c848deff61691
Author: lijewski <mjlijewski@lbl.gov>
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 6c256b24b7be0865ede37a7e059f56d9fed09ad4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Jun 17 11:50:14 2013 -0700

    Fix some comments only.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit 426d832f42b7d92b025be46ff25f2c4d116fd3ac
Author: lijewski <mjlijewski@lbl.gov>
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 cb27cce466d063d907e56752d6a8dea0f21cff73
Merge: 123ef66 790e009
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 15:19:32 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 123ef66a8c38f16a3d59d9fc65cf8541568ec19c
Author: lijewski <mjlijewski@lbl.gov>
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 2f7ebdff44129bc7ece830dcc115d00e6c9cd111
Author: lijewski <mjlijewski@lbl.gov>
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 46f1d5503b3d425e14428515689aa30a56782744
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 14:18:55 2013 -0700

    Changed the name of a constant.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 2a6d836746e15ce7988a632cb9c57dd5143019f1
Author: lijewski <mjlijewski@lbl.gov>
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 438e679074aaece9790e7feda12182d861514668
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 14 10:52:40 2013 -0700

    Some OMP tweaking.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit 790e00953bd6bf04f1e3117ea2ad70d5a3593263
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 64689c15cc8d811e6941b77a2985d2292d8522e0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 84ee0b81b1749b5d3b0726a3adaf596697a285d4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 17:16:22 2013 -0700

    Added some barriers.

Tests/C_BaseLib/tFB.cpp

commit 39b20d22173f392a7e6432c6962855483bb16e2d
Merge: 6cdda25 0cbea00
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 12:58:22 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6cdda2589ac71491e772250819f2a239ca918112
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 13 12:51:53 2013 -0700

    New FillBoundary() test I want to run.

Tests/C_BaseLib/tFB.cpp

commit 0cbea00c989b65aba3f5aa496a1bcb8f7468ca40
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9b870e7ebfaccd63ae8fa55d7f8723978a554df5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f87f7bd1befff79117e21dcc31c264f8aba3bbff
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c9387fa04fd1e2e505af6666ac436ddd219da63d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f2c700341ed2c93bd3dea97708b681227b8e9a86
Author: vince <vebeckner@lbl.gov>
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 71e317668bea8245ab3ec5385409a73a4ce71374
Author: lijewski <mjlijewski@lbl.gov>
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 2cae4d2ea8ef034387e4dd3c86460be95fbb635c
Merge: c668eac e503b0c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 14:08:37 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c668eac525136aa123f65cf8fb50d88414b9f68c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 14:08:15 2013 -0700

    Mods due to formal argument changes.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 6ee6cfccb53d6b751c59e48ce4159d705b31c8f6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 13:46:04 2013 -0700

    Destroy a boxarray.

Tests/LinearSolvers/F_MG/wrapper.f90

commit 55db139289b2b9f7a3d41f9c7fabb4e7597a3d4e
Author: lijewski <mjlijewski@lbl.gov>
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 9f19927c261cbea6b034a9dc6de0bf3c2c51dbd3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 12 11:01:27 2013 -0700

    Fix bug in s_simple_1d_nodal().

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit 797ef77b26dfa82f9fe55623448dd82ce40679fd
Author: lijewski <mjlijewski@lbl.gov>
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 1695d0f8675e36d592ff13ad0125b2e7e789c9cb
Author: lijewski <mjlijewski@lbl.gov>
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 e503b0c19f64f4d7eedebc172795f01ff58edb9e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 33c5295d776fb227e7d2113aeaad6cd038b48366
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f1c5af2405cf3a678fad67f0bde07732a5c265b5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c0db0c7f17ff1e8eedde56b4f51d73b28975a2af
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 10 10:37:41 2013 -0700

    A little memory cleanup.

Src/C_AMRLib/StateData.cpp

commit a5b7ad7d261e4a89d0eb65cbd08e94b685e2136c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 10 10:29:06 2013 -0700

    Fixed OMP bug.

Src/C_AMRLib/AmrLevel.cpp

commit 4c0c9bd13b58c007ce527f8a65943d08b7f15289
Author: lijewski <mjlijewski@lbl.gov>
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 f042e44f770952d7c2476ce98d4dd7438155027d
Author: lijewski <mjlijewski@lbl.gov>
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 94afa49e716e474b032f80a384bebade8906d2c5
Author: lijewski <mjlijewski@lbl.gov>
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 a21da84aca22c0deaa28456623f13e5a14ab6eff
Author: lijewski <mjlijewski@lbl.gov>
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 73a42622c1761b3559767e1a6b478d7c15db00ae
Author: lijewski <mjlijewski@lbl.gov>
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 ee3dddcf85d4a29336d163c82b31dc8e2337956d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 13:13:02 2013 -0700

    Named the critical section.

Src/C_BaseLib/BaseFab.H

commit 4ce4d9558951b47e1f3a8cd1746632911513427e
Author: lijewski <mjlijewski@lbl.gov>
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 c2490d4f51701ef97a0ed9545044de1c081123d8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 6 07:30:35 2013 -0700

    Fixed OMP bug.

Src/F_BaseLib/multifab_f.f90

commit cafc252f44d53c834dfd498accd3b5f1e8e54d81
Merge: 3f24251 3a50328
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 14:14:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3f24251a4875a23d8e86416b644d4ff07a9fbccc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 14:08:50 2013 -0700

    OMP over operations on boxes in boxarray.

Src/F_BaseLib/boxarray_f.f90

commit 580f62519eea2302a993e6353f950f858ffb5929
Author: lijewski <mjlijewski@lbl.gov>
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 3a50328bbea51e3057ddfa6ab25f459046b7a7df
Author: Ann Almgren <asalmgren@lbl.gov>
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 32119f256154e4b3b1dd95f2147ad456ad4c8c2f
Author: lijewski <mjlijewski@lbl.gov>
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 28ad2081a304210423a57665a8078b8619b3eeaf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 10:26:27 2013 -0700

    A little cleanup.

Src/C_AMRLib/AmrLevel.cpp

commit 1e603f7e921950ede47ef3f61b1800c56330d30f
Author: lijewski <mjlijewski@lbl.gov>
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 6a1407f1b961447eede7391632012eabd5654d45
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 09:21:53 2013 -0700

    OMP over faces when interpolating bndry data.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 7a4e1205e5343cbf7389f885c23baa6c1e23c771
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 09:21:15 2013 -0700

    Promote MultiFab::IndexMap() to be a public member.

Src/C_BoundaryLib/FabSet.H

commit a6305a177b38dd92a5cded071cf9066099002690
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 5 08:37:03 2013 -0700

    OMP over the tagboxes in a tagboxarray.

Src/C_AMRLib/TagBox.cpp

commit 4edded47889d71febdcd92146d535fca6ff58c23
Author: lijewski <mjlijewski@lbl.gov>
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 396f44f127ce9eef6207be6f6c61bd1968bede2f
Author: lijewski <mjlijewski@lbl.gov>
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 73cd34f0b7322531038d9ebfe170875631273156
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 4 19:30:32 2013 -0700

    Fixed OMP bug.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 1b0f0876b0850fb2c17e64b2bbea86d6eecac9ed
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 4 17:09:46 2013 -0700

    Fixed OMP bug.

Src/F_BaseLib/multifab_f.f90

commit 1ab4e7ce5056bef6f18c6156859a9f5759f09b95
Author: lijewski <mjlijewski@lbl.gov>
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 3bc5b9db6faf8ca0bd05e4b2b397ca1f807226fc
Author: lijewski <mjlijewski@lbl.gov>
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 1b6dfe31c98e44b11051447cfaf42de97d51cd4a
Author: lijewski <mjlijewski@lbl.gov>
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 448aab707c3f0b4d0c8567edd4a169e6cddb3b55
Author: lijewski <mjlijewski@lbl.gov>
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 2ffa8f8fae99bbd868eed1e7676496a9d8316899
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 10:59:04 2013 -0700

    Some cleanup.

Src/F_BaseLib/multifab_f.f90

commit bbf950c08d832f24a9882627847bbb94627879fe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 10:36:07 2013 -0700

    Added multifab_norm_l2_doit().

Src/F_BaseLib/multifab_f.f90

commit 9da8efe4dcb9ef3cdf2504abd04eb237ae91b2b2
Author: lijewski <mjlijewski@lbl.gov>
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 dff1e0b6f715cebe5f1629ab5a902db7e4f307e5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jun 3 09:18:09 2013 -0700

    Tweaking the OMP IF constaints on some loops.

Src/F_BaseLib/multifab_f.f90

commit 3a7f487c917cc14179866240d01be0a4d62270e3
Author: lijewski <mjlijewski@lbl.gov>
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 54c0a103dc72d666a0fb8af6e0511432a7421ec4
Author: lijewski <mjlijewski@lbl.gov>
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 096e32f62ca9912ff407326f97715e2a3cbb6441
Author: lijewski <mjlijewski@lbl.gov>
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 38101f54aca6a9f1ea8e95b091a9526a48ae923f
Author: lijewski <mjlijewski@lbl.gov>
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 dd9a855847c5fd44a1a7d8b4d4a14f0a5df95693
Author: lijewski <mjlijewski@lbl.gov>
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 7da8bbfe4c7dd473e0f31d360b0c5c1567e12022
Author: lijewski <mjlijewski@lbl.gov>
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 bf0e54d82cb488b19c457743e9ffaac5f638b3f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0df6d874f273c1dc48af26475ba16eaff204ca35
Author: lijewski <mjlijewski@lbl.gov>
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 4e04d617e0ebfa5ab703f90ec7c3c5f6020259f1
Author: lijewski <mjlijewski@lbl.gov>
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 6a7b00a968de43ebf312c6d8ae13085130d96688
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 16:23:17 2013 -0700

    More uses of only_small_boxes().

Src/F_BaseLib/multifab_f.f90

commit 2f4fcfceb64d32ce63687a79325ffa858e4e9421
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 15:40:12 2013 -0700

    disable nested OMP parallel regions by default

Src/F_BaseLib/boxlib_f.f90

commit 1db65f9c9af0f042aafa5c8acd00a0a69c2f1f87
Author: lijewski <mjlijewski@lbl.gov>
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 db5dbf4dda12cdf6ed7d703164a7f3b5be889f8f
Merge: 64400c1 132b40e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue May 28 14:21:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 64400c10cc58edb05996b9ffdd2f3d610dfe5ac3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 132b40ecd880706a18a55bc0e63c4d100bdfb110
Author: lijewski <mjlijewski@lbl.gov>
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 1eabaade19578f03e0bf9d78cdf9422c1906eb35
Author: lijewski <mjlijewski@lbl.gov>
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 3654e02a035c58e60a2782e636b5ba88b15bc57c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 28 11:25:04 2013 -0700

    Some OMPing.

Src/LinearSolvers/F_MG/ml_solve.f90

commit 226bb7377af99452b448c8422ad6fcbebf64a8c1
Author: lijewski <mjlijewski@lbl.gov>
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 cc88917e587855345f03bd95a0d537581d2723fa
Author: lijewski <mjlijewski@lbl.gov>
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 b477550a9030fe67982a0c243a4a69beb07856fe
Author: lijewski <mjlijewski@lbl.gov>
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 9e0883955c5c7614ee1928340cea428c8a1384e7
Author: lijewski <mjlijewski@lbl.gov>
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 2b0ead018d675153b8ed943fafe76002ad14bea6
Author: lijewski <mjlijewski@lbl.gov>
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 7773951a2ceb456daa20bc0b1651e8e8afbff3c6
Merge: c3de69f 9a6d4f1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 17:52:53 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c3de69f6f20704120ea5d4f14c32c1a2904b55ff
Author: lijewski <mjlijewski@lbl.gov>
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 9a6d4f1439e731bf378c14dcfd3cc791628eb200
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 27 16:56:41 2013 -0700

    Fixed bug I recently introduced.

Src/F_BaseLib/multifab_f.f90

commit 951dfa15f33f7602f511c90687e7e8728def5b05
Author: lijewski <mjlijewski@lbl.gov>
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 2b6c314341b4af4af0c14917eaacf836cdb5b71a
Author: lijewski <mjlijewski@lbl.gov>
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 722dd4418d62422399077a6cccf316f9cb4c9a02
Author: lijewski <mjlijewski@lbl.gov>
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 adb204210f62ba7b01e59e7d9a253958b1b1c5c3
Merge: 1a78c96 3ab615d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 18:26:17 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3ab615d344d279410ff595ce402ff1dffcc19ef4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 18:06:07 2013 -0700

    Fix typo.

Src/LinearSolvers/F_MG/itsol.f90

commit 1a78c9622f3976b2c36746544a9b903c8651ca8b
Author: lijewski <mjlijewski@lbl.gov>
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 66a475922146087cb1e65a8bcb1a8fcefbd0e215
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun May 26 10:22:54 2013 -0700

    Fixed typo.

Src/F_BaseLib/multifab_physbc.f90

commit b5aa9ad6fc6d5c54017f8af476f5593f952ad8c5
Author: lijewski <mjlijewski@lbl.gov>
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 1ef2abc3d3cb0c53176afc1618d63bd3ee8fe168
Author: lijewski <mjlijewski@lbl.gov>
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 0378c582d1693f3a5fec6bba42521c97131cbe02
Author: lijewski <mjlijewski@lbl.gov>
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 f1628a9b01659c48edea08a832c5ecabb75d2ca7
Author: lijewski <mjlijewski@lbl.gov>
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 fa120810211351a868cb3be78c16491fb37a9392
Author: lijewski <mjlijewski@lbl.gov>
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 b6fdc16e97cfee59078f17a7443ceffd0fd75d72
Author: lijewski <mjlijewski@lbl.gov>
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 a25117100200f43afb0e7816ba6a83ff1644a002
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 15:06:57 2013 -0700

    Removed some OMP loops that were effectively nested.

Src/LinearSolvers/F_MG/itsol.f90

commit 11e5f77e0cbcdae6bd3764db7a99053ef4e52883
Author: lijewski <mjlijewski@lbl.gov>
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 0eab51a2c459abf7c15789a64d3dfbaca93cdbd4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 24 14:45:20 2013 -0700

    OMP'd a loop.

Src/LinearSolvers/F_MG/mg_tower_smoother.f90

commit 8c48ff676527e722c6d1aa73be8df3fe5b62c161
Author: lijewski <mjlijewski@lbl.gov>
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 6b7b8f534c6c2e2ffc6e8ce0e092432cd1bbbf3e
Author: lijewski <mjlijewski@lbl.gov>
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 81cf47084c3177f8d4a59e220506f691ff10d219
Author: lijewski <mjlijewski@lbl.gov>
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 bd552bb790460d4e022a531cd0dd21eebb1a258a
Author: lijewski <mjlijewski@lbl.gov>
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 5a5ca149f19cc174ccecf21bd7b5da1469b188de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 17:03:28 2013 -0700

    OMP's part of BuildGramMatrix().

Src/LinearSolvers/F_MG/itsol.f90

commit 67d19501465683ad52826171fdbb1d3c44c09c8e
Author: lijewski <mjlijewski@lbl.gov>
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 976a65377ab9b00f22dec3e9d826773d4d352fd7
Author: lijewski <mjlijewski@lbl.gov>
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 28457b58dc5d3192420d8ef8465317de47bea457
Author: lijewski <mjlijewski@lbl.gov>
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 4baf41909ed6f256cb1aa2098a9a48cfe33288d7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 14:24:43 2013 -0700

    Removed some unnecessary setval()s.

Src/LinearSolvers/F_MG/itsol.f90

commit 90168ceb447c57354ffa7800f73d0101891f686f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 14:05:53 2013 -0700

    More cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit 49f03c5f66fc88f81476b1470c31a0cd11f34f67
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 13:28:10 2013 -0700

    Some cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit 78d2a9d97eaf91d894dcea712c6c078fab1f17fd
Author: lijewski <mjlijewski@lbl.gov>
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 34e55b4398a913b53259d3914c1fcb0e89b50859
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 12:51:38 2013 -0700

    Made BuildGramMatrix() a contain'd routine.

Src/LinearSolvers/F_MG/itsol.f90

commit e408fd54df8f0c6599329031a9515f2a00597bae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 22 12:21:37 2013 -0700

    Integrated in isinf() stuff.

Src/LinearSolvers/F_MG/itsol.f90

commit 7952390542446c4e5a4f167870e158f3e024b819
Author: lijewski <mjlijewski@lbl.gov>
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 c2a19c54caf394344c6dd0e6ed39f7a921d4f09a
Author: lijewski <mjlijewski@lbl.gov>
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 e7205738cd1730eda5fbb5a27901f43e16f4a7bc
Merge: 148b73d 9ad7447
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 16:13:09 2013 -0700

    Merge branch 'CA'

commit 9ad7447eb94e6c302df22eedc01417c962ccf647
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 16:08:17 2013 -0700

    Fixed bug I recently introduced.

Src/F_BaseLib/multifab_f.f90

commit 894194b67bf4e89dd1e7827e2349e0e5c9dc13ce
Author: lijewski <mjlijewski@lbl.gov>
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 148b73d0bb74ce5471d52145c694eb5b2147a0f8
Author: Ann Almgren <asalmgren@lbl.gov>
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 e738a00f9dc8125df32960c38a36179458724ecb
Author: lijewski <mjlijewski@lbl.gov>
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 d9c0f582813a5f07b9cfbc4c33da635052bc5244
Author: lijewski <mjlijewski@lbl.gov>
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 71a600e91100f48199a5e2d680c795876d4a4091
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 15:16:13 2013 -0700

    Some more cleanup.

Src/LinearSolvers/F_MG/itsol.f90

commit f7c56e0b7e3a92360f091562dee8bb4f6006ff20
Author: lijewski <mjlijewski@lbl.gov>
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 fccc5b301d06a9a75c30556b501e1bd3049c44db
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 14:46:24 2013 -0700

    Still working on CABiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 590cfa942b32a77dfca5b30155a9b1bd854aef8a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 13:56:33 2013 -0700

    Yet more progress on CABiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 4a25c354af37b117f3f37d8d282b1a3940746cb8
Author: lijewski <mjlijewski@lbl.gov>
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 69fc0393be96206f859e1d02cfd4179702d9c5a2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 11:21:39 2013 -0700

    Some work on building Gram matrix.

Src/LinearSolvers/F_MG/itsol.f90

commit 6d17fe496f0c9bce8a61b67d9b5afa1dffc77acc
Author: lijewski <mjlijewski@lbl.gov>
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 0bf12c8b8032f540d0ca7068ea8366558b402a3c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 09:27:14 2013 -0700

    Elided some more reductions.

Src/LinearSolvers/F_MG/itsol.f90

commit 6b39f1f5b2451427fb25ef7a21a2434eb94e7eea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 21 08:58:14 2013 -0700

    Some cleanup on the way ...

Src/LinearSolvers/F_MG/itsol.f90

commit 7f1f9bf0adc6a3fbb1e648ebed86d6494a8a1c61
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 13:34:33 2013 -0700

    Some cleanup of DGEMV().

Src/LinearSolvers/F_MG/itsol.f90

commit ee32b3587d37d68bd9d71bbe6b86d069043ea7f7
Author: lijewski <mjlijewski@lbl.gov>
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 7ff6e9defa6761187e754c545555cc0104243188
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 11:28:19 2013 -0700

    Added SetMonomialBasis().

Src/LinearSolvers/F_MG/itsol.f90

commit a46b0dcc4c7d45fde6007d857f85f1382534ef5f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 11:06:35 2013 -0700

    Still plugging away at CA algorithm.

Src/LinearSolvers/F_MG/itsol.f90

commit 27ab5f4157c60f3b443d0afe15f37ef865ec561e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 20 10:50:14 2013 -0700

    Yet more work on CA bottom solver.

Src/LinearSolvers/F_MG/itsol.f90

commit 64890ee9372e9f86e08ca02a425ec2e1f455c139
Author: lijewski <mjlijewski@lbl.gov>
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 cc4237382627f16e2112e962506e8a6d44dd66e6
Author: lijewski <mjlijewski@lbl.gov>
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 2bee4096af7856e3851867a0f516f793f77feefc
Author: lijewski <mjlijewski@lbl.gov>
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 7ce374d7a5087f7a69198f9073e14f5e21c1883b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 10:22:50 2013 -0700

    Removed some divisions.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 2b7f3625acb2ae88fcecbec570a2e5e1f4c5634b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 17 09:59:39 2013 -0700

    Some OMPing and code simplification.

Src/LinearSolvers/F_MG/nodal_stencil.f90

commit ce37e6b6a9614ed2e53c5fca5d5a2b1f1160d58c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 22:12:49 2013 -0700

    More OMPing.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit d343ee49c79767d617b898d6600677a63e0b37aa
Author: lijewski <mjlijewski@lbl.gov>
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 67fcafeba36fbb81109fb0d6aa2538a5f781411d
Merge: 69e4e47 9a2af17
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 20:19:56 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9a2af17876e458936e0d1a268d2465f87b684121
Author: Ann Almgren <asalmgren@lbl.gov>
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 69e4e47c5e4d06f79507e6f1d5beef877341bf97
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 16 15:44:51 2013 -0700

    Regularized some constants in the code.

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 371e587606502a51a863085621471a32f10df232
Author: lijewski <mjlijewski@lbl.gov>
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 a502c9a32fc97c04214e98ddbe63ee73cafd0626
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4ef86ac01f873184b0943aaa10ff8161cb7c716d
Author: lijewski <mjlijewski@lbl.gov>
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 961705032ddcb24de296b23365b69c50c649b405
Author: lijewski <mjlijewski@lbl.gov>
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 e01709b8d7dc76217de5d42a2dae6bf7c1dad6c8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 15 13:34:21 2013 -0700

    Tweak to output.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 5cc9af0c0da1931f62967d5bf6c2c0ec976e1595
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed May 15 09:50:28 2013 -0700

    Add zmq_suffix and hdf_suffix.

Tools/F_mk/GMakedefs.mak

commit 01af917f957c5ee1c2d3406ba3bab3bb49910f86
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1a91c3caa569fba252aa6b363afc0edd50b9a4d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 55d2f27d1a0656fe809cb6f7cbf358d713bed521
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6674cbc505978eb541884656abac5d2b971908fe
Author: lijewski <mjlijewski@lbl.gov>
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 280c73f7199087f779cbfce2253eee36aa7552cc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 12:27:20 2013 -0700

    Removed unused variable.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 7f7ddc284542807f21f5af0a6ab21ce069dd70d7
Merge: 77cbae2 a51a9bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 11:26:36 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a51a9bf5e4ee48daa3262478bfcf22c7c64e1f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 77cbae25d8986f3611cf30d2b3929341e934791c
Author: lijewski <mjlijewski@lbl.gov>
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 3506f17e4e7cb9a4de59a95d20f32f69214a081f
Merge: ebd6c68 24ca698
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:58:29 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 24ca69841f6849eaf0eb48fb94b2158ff9ed5d0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ebd6c680cd436791be2246ff881d746d341ec831
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 13 10:11:02 2013 -0700

    Little more OMPing.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit e36a72d42c466c0ec1bd6cab83d003d062f1fcea
Author: lijewski <mjlijewski@lbl.gov>
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 43327ff56ff64090578a1d2bfe9da6b81235c34a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:35:59 2013 -0700

    Simiplification.

Src/F_BaseLib/fab.f90

commit 8978baf2fd302eb42c7ac9d094d341cf79857fb6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:35:26 2013 -0700

    Fixed a bug I introduced earlier.

Src/LinearSolvers/F_MG/cc_stencil.f90

commit c5d1f770cd3d3295d709f557d569f3dad41e3b39
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 20:10:03 2013 -0700

    OMP'd max_of_stencil_sum().

Src/LinearSolvers/F_MG/cc_stencil.f90

commit b84ab0827e712c71b973a9c7d8d46b818a5900f7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 19:49:09 2013 -0700

    Threaded BuildGramMatrix() except for the reduction.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 3e85f7c21a89bd31ef7df191c222bd13c3c86d45
Author: lijewski <mjlijewski@lbl.gov>
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 ca65605eb9804200610f19562cf92e846e9cea86
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 14:19:44 2013 -0700

    Elided more reductions.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 702fc911f82c794d77ee040e2358580d04573914
Author: lijewski <mjlijewski@lbl.gov>
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 1cf3baeb2153b043d5bbc4ad698071d1633743cd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 13:39:29 2013 -0700

    Yet more parallel reduction elision.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 87886b683016df75a86befeaeb1b508d7eed96bf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 13:31:14 2013 -0700

    Some parallel reduction elimination.

Src/LinearSolvers/F_MG/mg.f90

commit 9c441778fdc0e56bde6bee5152665d9990ca7ee5
Author: lijewski <mjlijewski@lbl.gov>
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 a18d0e078faae604f9272f14f3061ffa7a74c2f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 10 10:47:57 2013 -0700

    More debugging & performance analysis output.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 1fe43e67e9bc4005cb6dc37c1ca946773113b969
Author: lijewski <mjlijewski@lbl.gov>
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 47207b01e3b828d93c48e8ac67d4350928c90da4
Author: lijewski <mjlijewski@lbl.gov>
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 c2eb369e12524e37e41e293a7b9faa9c3f8762d2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 17:21:51 2013 -0700

    Removed multifab "sh" from BiCGStab; reuse "ph" instead.

Src/LinearSolvers/F_MG/itsol.f90

commit fbb52b6ba2f664bf2d837e6d4831def1062f2bc8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 14:50:03 2013 -0700

    Some cleanup and code simplification.

Src/LinearSolvers/F_MG/itsol.f90

commit adbb38a653e834e9bebcf4c04eb1581a6cd48631
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 9 14:20:43 2013 -0700

    Elided a few more reductions.

Src/LinearSolvers/F_MG/itsol.f90

commit 01a869fea2ed7516c52712ddd7f350858e6d66e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 17:31:38 2013 -0700

    added reducelonglongsum to non-MPi build

Src/C_BaseLib/ParallelDescriptor.cpp

commit 3f8e0a23882271796fd38c94e3d3bee7cd3e1473
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 17:22:51 2013 -0700

    added -lmpich back

Tools/C_mk/Make.mpi

commit 5a844aafbf2e0ac7a130312edb9c4f769f38b2a1
Merge: 7253b6e 81d4ab6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed May 8 16:24:22 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7253b6e047a98d1d14a242ff0191c188ab4fdd29
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 81d4ab64be3f07210b7cdb4c8c3b4f8e7b98fbc0
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:20:25 2013 -0400

    force double precision plotfiles + other changes

Tools/RegressionTesting/Maestro-tests.ini

commit 6f29fa71d5e79c459d08e1a7ccf76877725833f2
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:19:57 2013 -0400

    ok -- for real now...

Tools/RegressionTesting/testnew.py

commit 64790a9df098f365b111cc9a613850254b088cff
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed May 8 19:03:57 2013 -0400

    self -> suite in the enw parameter

Tools/RegressionTesting/testnew.py

commit 75724a208a94e766e5f091b9f6f259adb050156a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 f4e01c450af9a9316356fb88ccf79fc3cc771abe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 8 14:57:09 2013 -0700

    Increased SSS_MAX from 4 -> 6.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 97fc5ba58847e5b3bbc8600c7d01925ccfbbc94d
Author: lijewski <mjlijewski@lbl.gov>
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 e264b37a6302f92ac10cde352537a590449ce34c
Author: lijewski <mjlijewski@lbl.gov>
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 48cacd5be198996464d9409a5f0d2311475913fb
Merge: a01919b dd52426
Author: vince <vebeckner@lbl.gov>
Date:   Wed May 8 10:01:24 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit dd524262c633d80ee13ddb4813ca35a9e9c5ca22
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 7 15:31:42 2013 -0700

    Some cleanup and improved comments.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit e434d16040fb3417f4fd140fc119487c62f39367
Author: lijewski <mjlijewski@lbl.gov>
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 3e3dc98688127339a485ac9457c84aab2d85582d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 7 14:37:49 2013 -0700

    Merged in Sam's latest changes.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit a01919b13ae77b45f6fab1b7b276b15e34cc1021
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 7 14:35:42 2013 -0700

    prof def.

Tools/C_mk/Make.defs

commit 2ef28d3731801663df798edbac25ffeb07739d3f
Merge: 44050d4 c098ccb
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 12:25:06 2013 -0700

    Merge branch 'master' into commprof

commit 471201209d31bac2197ea912a69a10e2eee6f5ff
Merge: 0ff9112 f8dfb7a
Author: Chris Malone <malone@ucolick.org>
Date:   Mon May 6 11:43:36 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 0ff9112f741a350ebb421e82de5597ca8019bb91
Author: Chris Malone <malone@ucolick.org>
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 44050d41cbec81a8d456291869d503dd4e43127f
Merge: e97c303 12f7007
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 11:28:04 2013 -0700

    Merge branch 'master' into commprof

commit c098ccbad32adc3d6fa1fecab5794e7ea780ffa6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 6 11:25:38 2013 -0700

    Still more include "file" -> include <file>
    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 e97c3037f3daf4bf729b84e3a8ba8a2d612d4bdc
Author: vince <vebeckner@lbl.gov>
Date:   Mon May 6 11:24:07 2013 -0700

    profiling doc.

Docs/Readme.profiling

commit 207f834e43f9b98396ddf3cfdbe5b4e588b5e4d9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 6 10:40:46 2013 -0700

    A little code rearrangment.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 12f7007da5691798ab9c7733640f28dcd921a382
Author: lijewski <mjlijewski@lbl.gov>
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 ca705cd1d2d0edeaece43367faced8ecc85a6be5
Author: lijewski <mjlijewski@lbl.gov>
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 e16c033b28e53d7a662f82774297b8cd5bff1058
Author: lijewski <mjlijewski@lbl.gov>
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 17840884621799089b7e4ce1e02b5a3b5057a373
Author: lijewski <mjlijewski@lbl.gov>
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 387713cb85ab3782890e968556b75b9c7fc35ae2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 13:58:58 2013 -0700

    Some more work on convergence criteria for CABiCG.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit b5933d22a140fd12276edc12d3acc544990929c9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 09:56:17 2013 -0700

    Be a little more careful about convergence tests.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 66879ba7c63922398265d0b3a808e0e49b17583c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri May 3 09:05:18 2013 -0700

    Removed some unneeded code.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 06e7663c74b229d3c9e030722b07d086ac7e61c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 19:57:04 2013 -0700

    Some refinrements and bug fixes.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8595a8351c6a587292c3149a13f596331c0c7bc4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 16:06:04 2013 -0700

    A little code rearrangement.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 7b4e51fdd5d15dc688d5b4723fbda33afcbb2128
Author: lijewski <mjlijewski@lbl.gov>
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 175035e00fc9a1c8f68a6694f81038c3c123ae8a
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:19:33 2013 -0700

    fix for serial.

Src/C_BaseLib/Profiler.cpp

commit edc5704f3f735189695cd17c2b67b53c6b4ce30c
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:09:20 2013 -0700

    added mf test code.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 31be56d7d8ba9a629a8f4b2d481a25fe321e93e4
Merge: e504802 a0064c9
Author: vince <vebeckner@lbl.gov>
Date:   Thu May 2 14:08:17 2013 -0700

    merge issue.

commit 7a7345eec0e3002e18096cfbfa5dbcbbf2efe15b
Author: lijewski <mjlijewski@lbl.gov>
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 561b456a58529c32b79b5f212e507cd4fb9f0072
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 2 12:49:54 2013 -0700

    Looks to be more-or-less working!

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit febf34dba7cc701a78c73e16a543f062cf36d587
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 17:20:46 2013 -0700

    Getting closer ...

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 5e991b8da18ba638acb91ee9a437f2b2c85fafee
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 16:40:44 2013 -0700

    Getting close to having something testable.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit d1e730808415f7e80d5c044ccedfb82f6b3c6dbd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 16:12:05 2013 -0700

    Don't think I had BuildGramMatrix quite right.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit ed2502db1b0b5132b9dfa79fec5e92e6483e8c9c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 15:39:59 2013 -0700

    Added BuildGramMatrix() code.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit c0b0eb745f4436aa2db05b9c9934fb48d93ce6dd
Merge: 0826964 9fd0aba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:51:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 08269643fc73491835985cf1a4d785defe18c492
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:51:41 2013 -0700

    More work ...

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8b42d53eb1f2d2ff68b3ea616c9b131726a4f57c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 14:42:24 2013 -0700

    A little more progress.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit b438010dfa1b79dcf6ce3dde7a6825cb23213739
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 13:52:41 2013 -0700

    More work on CA BiCGStab.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 9fd0aba43e1b8a27aa41899b6d5af7d073c0ac0e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 aff86402763139660e2da45e1811118f232ddbc1
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed May 1 13:07:51 2013 -0700

    Changes for Blue Waters Cray compiler.

Tools/C_mk/Make.Linux

commit c243c05f9e7506bad3397409774e4227fdec29c1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed May 1 12:58:24 2013 -0700

    Some work on CA BiCGStab.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 99cc2911d360a9f06075ca4a8fcdf2b0900d52e6
Author: lijewski <mjlijewski@lbl.gov>
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 f891f99279cf90d0045705fe7a6aacdcbc0fb7fd
Author: lijewski <mjlijewski@lbl.gov>
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 d498593a3c402ef476434d5cba63461a20cc5e15
Author: lijewski <mjlijewski@lbl.gov>
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 45c81dc7cfea1ec0d44e25dbcfbb410d06c0885f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ddc5679364051c4d64eda4faafe7ce3588e074d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a0064c941d8c661eebff80c7bc207a416a0fc976
Author: beckner2 <vebeckner@lbl.gov>
Date:   Fri Apr 26 13:42:11 2013 -0700

    new machines.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit e5048023140a2b3048d08de491f04ff879dfbb90
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 24 16:05:07 2013 -0700

    fixed ivLevel, ivLoc.

Src/Extern/amrdata/AmrData.cpp

commit dfddc5e4d79dc2e154ce2761f9f2ab0ac37c4201
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 157ec8b6874f848d9e17dd07b646972b9c4e975b
Merge: 1f5bc58 cf1bd96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 19 16:31:55 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1f5bc582d5b5062a15effdc354baf0d167a2d5d6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 19 16:24:05 2013 -0700

    Removed an unnecessary setVal().

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit c4ee28517991d07ac074ab6e7a7837e3a801bc30
Author: vince <vebeckner@lbl.gov>
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 cf1bd9648b6fa8eee58509ee3e579e0637b988bf
Author: Matthew Emmett <mwemmett@lbl.gov>
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 1752c72c714999d5c84d3fb1b28cf4319fcd70fc
Author: vince <vince@garnet02.erdc.hpc.mil>
Date:   Wed Apr 17 14:21:37 2013 -0500

    garnet.

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 797064623fdc7a2313ab210fdf8c1215391d9b75
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 059b5ab7f50dc142161b1ebf6cc951693fce142c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 10:18:29 2013 -0700

    OMP'd some more loops.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 0cbe501a249e7a01eb989d6f9b242dffafc4e4e6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 10:07:15 2013 -0700

    OMP some more loops.

Src/LinearSolvers/F_MG/cc_stencil_apply.f90

commit dbbf2b19a88c6bdc697f48d62899c94493bd6729
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 15 09:48:37 2013 -0700

    Some rearrangement to enhance vectorization.

Src/LinearSolvers/F_MG/cc_interface_stencil.f90

commit cba4f6b4e111d5f97f84a08ae6978792d5104a81
Author: lijewski <mjlijewski@lbl.gov>
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 ad26166016f8aa4122184af31285eba2bfeca8d8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Apr 5 13:33:09 2013 -0700

    beforecall.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit d41405989f32615bfafcbcd460812bf8be410cce
Author: lijewski <mjlijewski@lbl.gov>
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 040e63992bee1d43b551ce9963b823392c4990c8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 14:49:21 2013 -0700

    Replaced more divisions with multiplies.

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit d22d719a2512217c5bba618ec927e856bfa5db61
Author: lijewski <mjlijewski@lbl.gov>
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 741c342a24aa2e742e478e481ae2698da2df2202
Author: lijewski <mjlijewski@lbl.gov>
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 cb984487811cedfb58bbedf917c0f8989a0edcb4
Author: lijewski <mjlijewski@lbl.gov>
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 55fbcd1e27a42620f480088eae45df7778f1d7ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 4 10:51:21 2013 -0700

    Elide some reductions in BiCGStab.

Src/LinearSolvers/F_MG/itsol.f90

commit 387fbf5ef6fdbb7e3613a0cb34285207c23e6b12
Author: lijewski <mjlijewski@lbl.gov>
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 b46f26e91887e56943f0ed9f01ae76801414afb5
Author: lijewski <mjlijewski@lbl.gov>
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 d93bdcbc25a9d56e625eafd46e2542d1980956e7
Author: lijewski <mjlijewski@lbl.gov>
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 b50f2a69abca2f2a188fef5dfeeca76a57b5df05
Author: lijewski <mjlijewski@lbl.gov>
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 1ddbb0e143f0a2c67a3fd183a97b459564d3942c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 3 15:00:39 2013 -0700

    Replaced most divides by multiplies in apply().

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 1aadec77b71c2d701c0b0fac320b63942300c2a7
Author: vince <vebeckner@lbl.gov>
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 faf12c76e3601367807cb572cf5f663c8826ff33
Merge: 825de48 366cc61
Author: Chris Malone <malone@ucolick.org>
Date:   Tue Apr 2 15:08:27 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 825de481f94c5c66c6789cc189347b32cf7085a9
Author: Chris Malone <malone@ucolick.org>
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 366cc6184f51c01901affa9f27747c7334e93b41
Author: lijewski <mjlijewski@lbl.gov>
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 06e3e7166bc247d8e85fcf834d9fa9da4cde2f26
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 12:11:26 2013 -0700

    Cleaned out some unused variables.

Src/LinearSolvers/C_TensorMG/DV_2D.F

commit 974a5bd95d1b19b4e297a89c2200840972bc551d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 2 12:10:47 2013 -0700

    Added -Wno-maybe-unitialized flag to [f,F]DEBF.

Tools/C_mk/Make.defs

commit ede3d265f04bc95d2aff76019a95a90ed04ecfda
Author: lijewski <mjlijewski@lbl.gov>
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 d6818a9ecebe02fc7e99b9f46833eb532f5887de
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 16:40:33 2013 -0700

    fixed nfiles init.

Src/C_BaseLib/VisMF.cpp

commit 300a680b619b58947004a5ef7a3a1c5aa9c5ff58
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 16:39:12 2013 -0700

    fixed init nfiles.

Src/C_AMRLib/Amr.cpp

commit b72cb6d588301ba84c226723302e8b437bd20bfa
Merge: 793dc7b 826e47a
Author: jbb <jbbell@lbl.gov>
Date:   Mon Apr 1 15:07:19 2013 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 793dc7be6da2c3ef3558a946e682900741c47416
Author: jbb <jbbell@lbl.gov>
Date:   Mon Apr 1 15:06:56 2013 -0700

    fixed mpi path on mothra

Tools/F_mk/GMakeMPI.mak

commit 77a4d077f000a99bd18a4bc6bf8e61cdae14a5e7
Merge: e2856a1 9660773
Author: beckner2 <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:55:23 2013 -0700

    hera.

commit 9660773309011e99ef174fd59955e0fa3d5c969d
Merge: 8ad8e19 826e47a
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:48:55 2013 -0700

    Merge branch 'master' into commprof

commit 8ad8e193dab091f173d2065c6da5925afbaee330
Author: vince <vebeckner@lbl.gov>
Date:   Mon Apr 1 14:47:45 2013 -0700

    tweak for waitsome.

Src/C_BaseLib/Profiler.cpp

commit 826e47a33e08cce9d2eb51581b082f23c8a9a4b4
Author: lijewski <mjlijewski@lbl.gov>
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 279fdcfa07430ceb2679ed028f9054ba0a239257
Author: lijewski <mjlijewski@lbl.gov>
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 e2856a1a5ca31328f8d681b425c0e5d47f345446
Author: Vincent Eric Beckner <beckner2@hera840.llnl.gov>
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 2d70b9b6759409c9518b9c6485408337272f4d69
Author: lijewski <mjlijewski@lbl.gov>
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 8d398f598da36c5261c7164a992d93b00d606648
Author: vince <vebeckner@lbl.gov>
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 da914bb7c0bf83ee307d71a5eba1f4fe86b8ec78
Author: lijewski <mjlijewski@lbl.gov>
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 1a1e9bfd9acc37b6449afcfa3b6595c17048f7f1
Author: vince <vebeckner@lbl.gov>
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 3c106e75fbabb5849c053681ef238aa294c920a8
Author: lijewski <mjlijewski@lbl.gov>
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 f3ad326fc27fa80b4c4da4ff9d69b202429bd6df
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 20 10:42:56 2013 -0700

    added more profiling.

Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp

commit 60633b76ff88d852ca6b459bbfa3aedb182b2988
Merge: 024965a c259ab4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Mar 18 14:18:23 2013 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c259ab401468216cac98d509aab5934ac94882ea
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 024965a93e7cbd64c3e1cf9a762b23e0fc748c65
Author: lijewski <mjlijewski@lbl.gov>
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 4360d23e78443c87f2f7bd169137ebad558d46df
Author: vince <vebeckner@lbl.gov>
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 6dfd54d5ad3da26379fe903acf5e0eebdb7c584e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3579ca64073aa54ffa5732dda60d5d36f70840bf
Author: lijewski <mjlijewski@lbl.gov>
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 b606bebca83668aa104173c5cedb5149bcafd8ec
Author: lijewski <mjlijewski@lbl.gov>
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 33fe9d163c228fc20eaff104b1a1cbad8ba069eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ab532127041f08d69b2514ccd2e5d4c972412751
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 14 13:38:47 2013 -0700

    A little cleanup.

Tools/C_mk/Make.defs

commit 6b01d33aebfee08a107f60591dfdbf041eff4c06
Author: lijewski <mjlijewski@lbl.gov>
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 4f349682d28733aa12c55203f88ac1fbe4215489
Author: vince <vebeckner@lbl.gov>
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 73493ac184493dac606206ccd6f76fe139712a2c
Author: vince <vebeckner@lbl.gov>
Date:   Mon Mar 11 16:21:37 2013 -0700

    made call orders consistent.

Src/C_BaseLib/Profiler.H
Src/C_BaseLib/Profiler.cpp

commit 8ca4d061887c0f6ecedb3b26d1af9d71a7f84500
Author: vince <vebeckner@lbl.gov>
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 f8dfb7ae394673ef67df01b8e7469a311904a4c4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Mar 4 13:00:08 2013 -0800

    Option to dump a plotfile for errors in finite-difference fcompare

ffdcompare.f90

commit 5890360fb18d9746e22bedaea0f93056d4619e21
Author: vince <vebeckner@lbl.gov>
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 9332aed6a6840277207161f8a031c6c92dfae170
Merge: 3f2e95e 9b251b4
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 28 13:31:30 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3f2e95eaedfc00ce1608f5e0607be5143bd18724
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 28 13:31:24 2013 -0800

    Add profiling to multifab_saxpy_3.

Src/F_BaseLib/multifab_f.f90

commit 91c02a2ebfeddfad376a21606ffe05b7d38ac824
Author: vince <vebeckner@lbl.gov>
Date:   Thu Feb 28 12:01:51 2013 -0800

    barrier changes.

Src/C_BaseLib/Profiler.cpp

commit 95f5e1338ccdddbbd21d0f013299014fbd26a985
Author: vince <vebeckner@lbl.gov>
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 9b251b45a80485f5bfe095b59c6e5cdf192f86f4
Author: ajnonaka <AJNonaka@lbl.gov>
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 3881653a26edf916b66ca57f0133eadfe718a2ad
Author: lijewski <mjlijewski@lbl.gov>
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 80f34879688937a2c373f940b86af362d9be11d6
Author: lijewski <mjlijewski@lbl.gov>
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 9d4649330339d566f6b077d01d01d77767ae0bf9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 25 13:37:14 2013 -0800

    fcompare for finite-difference results

ffdcompare.f90

commit f0c00a0ac18ad7bbf34689e53a27ccda11f7f421
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Feb 23 17:19:02 2013 -0800

    Add GetParticleData access routine.

Src/C_AMRLib/Particles.H

commit dbae66051298f1ca8183eda4d85b41a6cc91ff03
Author: Michael Zingale <zingale@localhost.localdomain>
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 38bfb172a48fc88086cdf85bf3c30e9a1c30590e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 21 16:49:10 2013 -0800

    A little cleanup.

Tools/C_mk/Make.defs

commit a1eb3051c3eac2c490330d756462a4bdbf61bd5c
Author: lijewski <mjlijewski@lbl.gov>
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 a278ee2a5a6dbe80fa403ce326e687c6d8692798
Merge: 4275788 7624abc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 20 12:54:05 2013 -0800

    Merge branch 'redistribute'

commit 4275788b576d8c2a415efcc6783db10e8bfb9eb9
Author: lijewski <mjlijewski@lbl.gov>
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 dccc407d89aa581b3de904d32fb5c77766c2ee45
Author: vince <vebeckner@lbl.gov>
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 8ccc515e0b063f342a3666373589d5023fba11cf
Author: lijewski <mjlijewski@lbl.gov>
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 0e7465f1c492430ae5851c66c1c90bfec00c4ab0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 19 15:10:31 2013 -0800

    Added edison stuff to mirror hopper.

Tools/F_mk/GMakeMPI.mak

commit 604b151e08337cb57dd9dd09163facbf1b606ee1
Author: vince <vebeckner@lbl.gov>
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 d11e171d6f9fe243bfe95272e0bd75b690f3c25c
Author: lijewski <mjlijewski@lbl.gov>
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 3775471547d77db2a85912fe38ea90c1fde7680a
Author: lijewski <mjlijewski@lbl.gov>
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 c1cd4951826853042a6c729d37e34858d83f6ec2
Author: lijewski <mjlijewski@lbl.gov>
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 939ab6896902adbe59677a10b133ac4de853f4d3
Author: lijewski <mjlijewski@lbl.gov>
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 05c043a87facb899b9387296f40094ebe67ee90c
Author: lijewski <mjlijewski@lbl.gov>
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 7624abc0d210bc021402b264ab325b895ac0066d
Author: lijewski <mjlijewski@lbl.gov>
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 8515b4de012706fb2c9ca72325c3c9eee3d6721d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Feb 16 19:08:13 2013 -0800

    Some cleanup.

Src/C_AMRLib/Particles.H

commit 3f6cc2a0782ca958664fbe51301e31799f38bc66
Author: vince <vebeckner@lbl.gov>
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 65161c9643c88e2821429dadcd76f5e5d7a701c1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 14 11:22:43 2013 -0800

    A little cleanup.

Src/C_AMRLib/Particles.H

commit 85c702ddb88375e12b70884a759a3a8dc43306f6
Merge: 3fcf2c4 ea61233
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Feb 14 13:44:55 2013 -0500

    Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib

commit 3fcf2c41479e6ea85b25289dbe26f7ceead27540
Author: Chris Malone <malone@ucolick.org>
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 ea61233091aab3e62ad309605cb37b088fd265d0
Merge: fe48fb4 572c6fa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 16:02:13 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe48fb4d235d3f00f1c9d00d8fc936d813b33ce6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 16:01:55 2013 -0800

    Made the destructor for ErrorRec virtual.

Src/C_AMRLib/ErrorList.H

commit e57d15421cd4da966fe4d6c0ab2d583fd4ded9b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 15:53:24 2013 -0800

    Little more work on AssignDensityDoit().  Still needs testing.

Src/C_AMRLib/Particles.H

commit 8d64711803f7887f73057fee5eb43451e3be875e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 15:14:08 2013 -0800

    More work on AssignDensityDoit().

Src/C_AMRLib/Particles.H

commit 572c6fa76f852784f50db0673ee8039b8cfe01bd
Author: Chris Malone <malone@ucolick.org>
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 77d59c903811cef6709ca81f698e971c332a1a44
Author: lijewski <mjlijewski@lbl.gov>
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 c24266ef90e048512423999b27602658961c2787
Merge: e168957 a672ff2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 13:07:35 2013 -0800

    Merge branch 'redistribute'

commit a672ff23362b41879e78701280acc6341dda27ea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 13:04:15 2013 -0800

    Merged RedistributeMPI() into AddParticlesAtLevel().

Src/C_AMRLib/Particles.H

commit e1689575c6998daef05df10b3e81328344c7ae18
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 13 12:47:58 2013 -0800

    got around Cray compiler bug

Src/F_BaseLib/multifab_f.f90

commit 125d3c1cdbfd8e28fc0dbe873e6c124537ee4bd0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 13 12:25:52 2013 -0800

    Merged in RedistributeMPI().

Src/C_AMRLib/Particles.H

commit bcca699258f1db9b0f2bdc0c729634cc0f6939fc
Author: lijewski <mjlijewski@lbl.gov>
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 c06a9bcf16d85f2eeb1f1aafe83f0afea01c1720
Merge: 7e9cdc8 e08b524
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 16:52:13 2013 -0800

    Merge branch 'master' into commprof

commit 7e9cdc826e086e717612820dff8b2b107a40f8d6
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 16:51:10 2013 -0800

    some changes to the output format.

Src/C_BaseLib/Profiler.cpp

commit 9f4fc50722b94d92a774950eb90c66f2029cc9fe
Merge: 90779ab 12ca0c0
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 11:03:52 2013 -0800

    Merge branch 'master' into commprof

commit 90779ab3ddab750077297534f253125c89e95c0f
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 12 11:03:35 2013 -0800

    more support for the output parser.

Src/C_BaseLib/Profiler.cpp

commit 2ef3a07d3fb1af8aea4e189f7b2dd0261655ca03
Author: lijewski <mjlijewski@lbl.gov>
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 7c462d5e5380cbdf93a3505f5a3aeff6697ee17b
Author: lijewski <mjlijewski@lbl.gov>
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 16d4d8f92d16c1f9b8a25e7bed8f11e3e98443b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 19:55:41 2013 -0800

    More work on Redistribute().  Getting close.

Src/C_AMRLib/Particles.H

commit 88e42c14a834ee906be74d77a3dafc5f551e004b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 19:24:06 2013 -0800

    Yet more work on Redistribute().

Src/C_AMRLib/Particles.H

commit 741831bc81710424183d3dd4f7713eb296b4d7e9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 18:59:35 2013 -0800

    More work on Redistribute().

Src/C_AMRLib/Particles.H

commit c1377b1b5cc2fb775294e8b7be7d4970c3cedafc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 11 18:21:59 2013 -0800

    Some work on Redistribute().

Src/C_AMRLib/Particles.H

commit 34a763c9a1c5665be193dc36b60382ed3f3e3815
Author: vince <vebeckner@lbl.gov>
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 e08b5249366da9e54349348079173708ac36ff41
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 14:56:25 2013 -0800

    Reverting out previous mod.

Src/C_AMRLib/FLUXREG_3D.F

commit 16c58e149add2f89fd2b3f444e6b4b54992404cd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 14:03:51 2013 -0800

    Some OMP tweaking.

Src/C_AMRLib/FLUXREG_3D.F

commit 1e91342411fc339295201b6b18f07a28f9b2f45b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 8 13:45:58 2013 -0800

    Some OMP tweaking.

Src/C_BaseLib/SPECIALIZE_3D.F

commit 2c3a232c307a0d89f5bb4268a9be3d55483e2b5c
Merge: d3081ba 18dea58
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 8 10:31:24 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d3081ba20aff11eeca17d46d92ac89fa15cbf3bd
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Feb 8 10:31:06 2013 -0800

    more bc types for stokes_preconditioner code

Src/F_BaseLib/bc.f90

commit 18dea588526e585d27beddb5dd7352055356f2ec
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c5fa66d3ec72701e9ce95599d606a54aa535003
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ca9315ee5d8e29cdf308af92d008a7d87f2d3138
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 7 10:46:33 2013 -0800

    Python: Minor tweaks.

Src/Python/pyboxlib/fab.py
Src/Python/src/fboxlib.f90

commit 03928a62a75bbf38383ee495c49fd5a92b3cf26e
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Feb 7 10:45:19 2013 -0800

    Remove volume from finite-difference convergence tool.

Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp

commit 271152bb93637650f3c151a1994eb27a62e53a91
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
Date:   Thu Feb 7 11:41:20 2013 -0500

    More faverage edits/fixes to the RMS calculations

faverage.f90

commit 77cefe1f80c3417de4b390a495c273c8a150acbc
Author: vince <vebeckner@lbl.gov>
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 38e6ddea5257306bb372b36fb5d5bec9fc6df94f
Author: vince <vebeckner@lbl.gov>
Date:   Wed Feb 6 16:19:02 2013 -0800

    implemented nfiles for bl_prof output from all procs.

Src/C_BaseLib/Profiler.cpp

commit 45e5d650a6b927d392fb029c965d59fa3de5c80a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:14:52 2013 -0800

    added OMP to setval in F_BaseLib

Src/F_BaseLib/fab.f90

commit f333857d01b7e4f337e5c6671cb662ba9f109a5b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 16:14:00 2013 -0800

    added OMP to sum_d in F_BaseLib

Src/F_BaseLib/multifab_f.f90

commit 20edf70cb5d2a66a59e80f73c16e240505f705b7
Author: vince <vebeckner@lbl.gov>
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 5149ee87dbb63819fe6c7945a06d8c74ab15b5cc
Author: Adam Jacobs <adam.jacobs@stonybrook.edu>
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 9ac927beb5db2cc274cf965e4b8de7efcab13533
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 14:23:54 2013 -0800

    OMP multifab copy in F_BaseLib

Src/F_BaseLib/multifab_f.f90

commit 148ce3ba54c552eacc3750c528187541f8a3797f
Merge: 58097fd ac241ee
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 13:08:26 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 58097fdf3756d749c6b08dd99e7a652fa30be7e7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 6 13:07:25 2013 -0800

    Collapsed some OMP DO's.

Src/F_BaseLib/multifab_f.f90

commit ac241eecb151740562be88e69e1473fbc0a24f9c
Author: cmalone <malone@ucolick.org>
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 e877f5d61610254e13d436343117314c51db5594
Author: vince <vebeckner@lbl.gov>
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 7d407b1b3cb0d4e64fe4ee53e7ad3ac6ea036511
Author: vince <vebeckner@lbl.gov>
Date:   Tue Feb 5 15:58:15 2013 -0800

    handle profiled names that are not on the ioproc.

Src/C_BaseLib/Profiler.cpp

commit 99c5f77c12ff07e229972af1b758bee8a4b58cd6
Author: vince <vebeckner@lbl.gov>
Date:   Mon Feb 4 15:05:19 2013 -0800

    synced profiled names list across procs.

Src/C_BaseLib/Profiler.cpp

commit 13d89772ba000a86fec0e8002b419ad47ee24d46
Author: vince <vebeckner@lbl.gov>
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 4c2fd37875d699f4b5ade58a48da2de60c430890
Merge: 6c2ec65 7444718
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 1 13:51:28 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6c2ec659ef23d017647ef1dbfe0661edae35e182
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 1 13:51:16 2013 -0800

    Add more functions to ParticleContainerBase.

Src/C_AMRLib/Particles.H

commit 744471833e4a5c292624f9da6409d0166f216240
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 9234f2877ce1cf6137919df659f4fe21f2d5c083
Merge: f5768a8 feb2d00
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Thu Jan 31 18:50:36 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f5768a85a4c704cc49c4a168745dc8619a4daeea
Author: Michael Zingale <zingale@localhost.localdomain>
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 1c342da0e96130389eac7bc758001ea4e394f4d2
Author: vince <vebeckner@lbl.gov>
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 feb2d00b0c1f8c9ffdc49e964310bb127de90d05
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Jan 31 15:37:34 2013 -0800

    Add new functions to the ParticleContainerBase.

Src/C_AMRLib/Particles.H

commit 05b78547a618fc45b76bd0b7fbcc5dd926dc6200
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 2698d6a340bb52f76db0980140ea9616dd40a9ae
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 17827dea8f93235473ca0bfc17376f82eb8ce973
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 31 10:13:11 2013 -0800

    Tweaks to InitFromBinary().

Src/C_AMRLib/Particles.H

commit bbe234933c6774f679d0656a5f0ea64d3f3400a3
Author: lijewski <mjlijewski@lbl.gov>
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 58f1cdb29aa8548dca67e81d6b38d7863c78c3f6
Author: vince <vebeckner@lbl.gov>
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 5c370b577b1a62e7b42ebfffc2b86254cc72e330
Author: Ann Almgren <asalmgren@lbl.gov>
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 2634747cdc011ae2bc39dce8106a881549b4fc42
Author: Ann Almgren <asalmgren@lbl.gov>
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 75acffefbc0b98bcee358249fa42683d4fed72f8
Author: lijewski <mjlijewski@lbl.gov>
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 1da5946d54ba4f4067328688ca037c5dddbab1e0
Author: vince <vebeckner@lbl.gov>
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 12ca0c07d7cfc275a5f534376e271a3808c676f6
Author: Ann Almgren <asalmgren@lbl.gov>
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 dc824bc2e6222e504e481a91b78c2c8358907703
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jan 29 10:29:42 2013 -0800

    Fix comment about Nprocs > ngrids.

Src/C_AMRLib/Amr.cpp

commit ee3de04615987764b7e8c185df027119018cb5b0
Author: Ann Almgren <asalmgren@lbl.gov>
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 2548a77c865d493384939f59ab232986e78d718d
Author: vince <vebeckner@lbl.gov>
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 1909ba20e7029cf8759ae213d1a89921891813b8
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 25 14:20:34 2013 -0800

    eliminated warnings.

Tests/RoseTests/CPP/NullTransTest/PROB_3D.F

commit a7eb867e646425930fd626b6140353f2504e82a5
Merge: b530a96 0ac36b6
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jan 25 14:15:49 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0ac36b671119171203d90e254dcbedf0147b30bf
Author: vince <vebeckner@lbl.gov>
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 b530a9669bfccce50dfb35890da5bc3b3cffc02b
Author: Marc Day <MSDay@lbl.gov>
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 51dc44e104d9f04689939bdaf6c46c5e697406cc
Merge: fd55619 28e0d6a
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 24 09:50:16 2013 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fd5561989cea06a1bb9d6b53f8b889ab0ad080fc
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 24 09:49:53 2013 -0800

    Bad default value for bndry_comp

Src/LinearSolvers/C_CellMG/LinOp.H

commit 28e0d6ae9d92fe3418092c3e9758f4b5c8fbcd4f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 15744a654b628ea3d70522108b6357f1a696f459
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 24 09:21:11 2013 -0800

    Update makefile for Intel 13

Tools/F_mk/comps/Linux_intel.mak

commit 4d8a71d97b550f2b2f10f54242be3637a74e053f
Merge: d852bc8 d573eaa
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 23 18:37:46 2013 -0800

    Merge commit 'd573eaa'

commit d573eaa80bed94e3812ddc6174516ff5caa453e0
Author: Marc Day <MSDay@lbl.gov>
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 d852bc8db22b510d4e1e8cf10e591526ce8b5727
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 23 11:01:39 2013 -0800

    More OMP to the nonblocking multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90

commit f9139d1589d48baf50ef1b70e671635c14c65e3f
Author: Chris Malone <malone@ucolick.org>
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 65918d5cd55b34dbfc97bbfe63810bd6fe0e1d9f
Author: Christopher Malone <cmalone@titan-ext5.ccs.ornl.gov>
Date:   Wed Jan 23 12:40:15 2013 -0500

    titan updates

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 259ade08c4e2342ef9d21013e26e2df830df3819
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 13:41:01 2013 -0800

    OpenMP part of nonblocking fill_boundary

Src/F_BaseLib/multifab_f.f90

commit 72f3d964dffcdd787a182295755185f197ef3a04
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 22 13:13:13 2013 -0800

    OpenMP FAB_CONTAINS_NAN and INF

Src/F_BaseLib/fabio_c.c

commit 63db3471e7d60d26b9b7e7a8261ddcff6c37a659
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 18:53:04 2013 -0500

    remove python_plotfile

python_plotfile/vis.in

commit fb04d09cf5d79cb98f85079614e16f4909b0a163
Merge: 021ac57 a1e5c2d
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 18:52:39 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 021ac572e71103f817a6697bff137dc339cf9e39
Author: Michael Zingale <zingale@localhost.localdomain>
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 a1e5c2d392a0cc19c2d09fa9ae5070c2365c1d17
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 16:10:02 2013 -0500

    fix a comment

python_plotfile/plotsinglevar.py

commit 653b8856fba5055df2a77d60ade77a2e4976f760
Author: Michael Zingale <zingale@localhost.localdomain>
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 3f53bad9815681187777ff8dd5a2f5ea2d43ef38
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 20 13:32:16 2013 -0500

    sample runtimevis.py inputs file

python_plotfile/vis.in

commit 99b6f7281191aa2776181c0bd8af8c084c3d636a
Author: Michael Zingale <zingale@localhost.localdomain>
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 b23fd6586125274ace6895e4f4ed6b74c28e96d2
Author: Ann Almgren <asalmgren@lbl.gov>
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 4146900c2a5d8454fad9a5ad175e440daaf2c8af
Author: Regression Tester account <regtester@battra.(none)>
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 c93cd91c0e31f3756a15d389afbd38ae8def76ad
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jan 15 16:05:14 2013 -0800

    changed flags for fortran.

Tests/RoseTests/CPP/NullTransTest/GNUmakefile

commit 45d311bb0bee7f40300816f6b81549c38c1dd3e8
Author: vince <vebeckner@lbl.gov>
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 244eba0af80874f9bb56812409e9317bd48a5ac0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jan 14 10:00:33 2013 -0800

    Compile fillfab.f into tFillFab.

Tests/C_BaseLib/GNUmakefile

commit 89943ef523db39f1c682f267a2339fe7600ad791
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 21:16:34 2013 -0500

    add time

python_plotfile/runtimevis.py

commit 088f60c564482444511be55fc7f3acd86cfb741c
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 20:44:15 2013 -0500

    looking prettier now

python_plotfile/runtimevis.py

commit 958d8f47c126673122b0a23070c82c9ac3aea90a
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 20:29:57 2013 -0500

    basic functionality working

python_plotfile/runtimevis.py

commit 14a0236bb6b693854a9a482f532f8bb6adb9d6e5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Sun Jan 13 18:21:10 2013 -0500

    more progress

python_plotfile/runtimevis.py

commit 7a884a82f0c45448c137f13ae8862b0147f45277
Merge: 5a5a16a 23ec5dd
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 13 18:09:28 2013 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 5a5a16ab51d4d8260e033c28ce3c73e06c03161e
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sun Jan 13 18:00:08 2013 -0500

    start of a runtime vis script

python_plotfile/runtimevis.py

commit bc6b95a682ca1d6f43dcbebfc2de1427c11d0f05
Merge: 4df0ea4 17ca07d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 10 16:52:27 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4df0ea4255715ca6fdf2609411fd11ba498e7ee9
Author: ajnonaka <AJNonaka@lbl.gov>
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 17ca07d9fe5f6afe51abbcf9ba22682cc6e54579
Merge: 512f17e 40a5cdb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 15:21:54 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 512f17e242bd692298664d9d6ec6db07c808aab5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Jan 9 15:21:39 2013 -0800

    local_only --> only_local so declarations match.

Src/C_AMRLib/Particles.H

commit 40a5cdbc91958e240afe9f0325dd24cde700b425
Merge: 4e0ff44 32f22db
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 9 14:49:16 2013 -0800

    Merge branch 'streamretry'

commit 32f22dbe5022870475461a1e6716c55e8dff60d6
Author: vince <vebeckner@lbl.gov>
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 4e0ff449815c11d4bebacfe26e0ef69490b70566
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 8 09:23:45 2013 -0800

    Check in with tMF enabled not tFillFab.

Tests/C_BaseLib/GNUmakefile

commit 24b443dbcdd195378c05b8fb4b25a0931e598729
Merge: 461a347 5ef5b89
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jan 8 09:05:16 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 461a347f0e583ba0886369405b8fab866cb69db6
Author: lijewski <mjlijewski@lbl.gov>
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 5ef5b891d45a5993bf62e142da8020f37138c921
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Jan 7 06:50:39 2013 -0800

    bugfix; referencing wrong optional argument

Src/LinearSolvers/F_MG/mg.f90

commit 5fd57d0dc32fc7193496914874a98f3ba833cddc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 4 16:54:09 2013 -0800

    Added -rose:openmp

Tools/F_mk/GMakedefs.mak
Tools/F_mk/comps/gfortran.mak

commit a39cbc788a0f69881b00c20c6b10450a4168414d
Merge: e04311f bb2bbb7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Jan 4 15:38:32 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e04311fe68b6768955c5ef999a07d8029693bec2
Author: ajnonaka <AJNonaka@lbl.gov>
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 bb2bbb79b4c14120f673bec32e45adf55c06e2c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 16:40:08 2013 -0800

    Made make for ROSE again.

Tools/F_mk/GMakedefs.mak

commit 90b87096d92b66f74a26b595dd804a9375a9c361
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1cb1b764c7406167170b3e044cde90cf3a77179d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7df762f58437c1e113d25dc61ac4dbc87577466f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 3 12:11:44 2013 -0800

    Fixed OMP bug.

Src/F_BaseLib/create_umac_grown.f90

commit c1fc023b538ab23afe01665ee08cf5538fd42d21
Merge: 1d48013 06319b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 3 10:45:58 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1d48013ee9ae746c5baf62606e22cefcb8c114eb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 06319b1affdf3905365f01dab85b8b663d3767d3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 3 08:42:36 2013 -0800

    interface changes to simplify mac_applyop

Src/LinearSolvers/F_MG/mac_applyop.f90

commit 61772f83e41e086d03d103a7eaaed5eb6011650f
Merge: 3c411ee ccdc04d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Jan 3 08:26:29 2013 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3c411ee6f66b73e39c4fbd4b1065a5cb2ea1d331
Author: ajnonaka <AJNonaka@lbl.gov>
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 ccdc04d9d5ceacda2f5981f882e751d5c5ff35bc
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jan 2 19:05:39 2013 -0500

    explain Real in C++ and dp_t in F90

Docs/GettingStarted/GettingStarted.tex

commit 152e05f999fbcb28b40da8a1ea3e8fa24f1dd2d0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1e65c3085945486b3f9c5dc26d3d13250bd36cb9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 133151e6c4a6cfd847248608850cd78d8b7013a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 59d79b962506492ffedc6fc1120d4dc369a0a5f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8cf767958888d158473d7f9102582d491b1f4879
Merge: 6b4e6a0 d7d6096
Author: vince <vebeckner@lbl.gov>
Date:   Wed Dec 19 16:12:26 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6b4e6a01cd699a548ef501ca05a1fbf64b2baf3a
Author: vince <vebeckner@lbl.gov>
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 23ec5ddc038f93cfd25fbaffc14a0587fab8143a
Author: Michael Zingale <zingale@hopper10.(none)>
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 d7d6096ea9cde70521ed2682107a8324ce4ca2ba
Author: Ann Almgren <asalmgren@lbl.gov>
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 b74c7559777ab885d59661a563f1c5beaa24b176
Author: ajnonaka <AJNonaka@lbl.gov>
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 9e66e3bf514d9860c91c9aedd60bc2edad100992
Author: ajnonaka <AJNonaka@lbl.gov>
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 87b1d9fb96b632f2213517d02bc4b9faab1328eb
Author: Ann Almgren <asalmgren@lbl.gov>
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 0051502ffd2c47acb44277045c37f64ee45f52f7
Merge: cd60098 7b4de0b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 13 17:23:37 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cd600988335b932514ae5fb1f97b86decdf67fe2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7b4de0b0de9ca680eeef723e0c585e16ded1402f
Merge: 3492052 cbf39e3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Dec 13 11:00:06 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3492052044897b9a06c9b28431e95e780d0541a4
Author: lijewski <mjlijewski@lbl.gov>
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 cbf39e333cdcc04cf6fd5fa8fa9ffd68457e17a1
Merge: 30d784d be842cc
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Dec 12 19:51:21 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 30d784d45b2c145ebac8f02a3180860a97fee062
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 be842ccfa9eaed33fbeb01302be7e42ecde34f11
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 16:16:06 2012 -0800

    More work on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit d7809cad5d32ecb4713f9549153c150b460feb1a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 15:57:52 2012 -0800

    A little more tweaking on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit 62e4239feb44f4002f565fae4a1c7a0e8abb7e2f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 12 15:52:27 2012 -0800

    More work on InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit 2393c0a7c890519f94f8982e34f4fbe356cef5da
Author: lijewski <mjlijewski@lbl.gov>
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 f73c8c9d353307c9be9d1508fab0a1a7650fcb6c
Author: Ann Almgren <asalmgren@lbl.gov>
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 7297bdb45b8638af5ccd26082d2c864f32835e6e
Author: Marc Day <MSDay@lbl.gov>
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 2cc1cafe172ea29b9c4f3621b634eb3ee37ed36c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 16:19:52 2012 -0800

    writeavg pct fix.

Src/C_BaseLib/Profiler.cpp

commit 4f9841bd9f6baa312b7455aab10922972d2361dd
Merge: 0f04810 43d6fbd
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 15:07:00 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0f04810313ba6679973c5164595c512b002bb372
Author: vince <vebeckner@lbl.gov>
Date:   Fri Dec 7 15:06:28 2012 -0800

    fixed writeavg percent.

Src/C_BaseLib/Profiler.cpp

commit 43d6fbdacc4c485e63299252a44f03fb5a1dd434
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 7 14:53:38 2012 -0800

    some profiling tweaks

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/ParallelDescriptor.cpp

commit 67a0b7721855a1d6271160e2f91250f4b7b18e57
Author: lijewski <mjlijewski@lbl.gov>
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 545dc0d24927b34f97e383c1738cb1a54fcfb0d3
Author: lijewski <mjlijewski@lbl.gov>
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 bac2c145e6fa3ffb4676e4ab73d20bde9b050927
Author: lijewski <mjlijewski@lbl.gov>
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 d9a0afb2fe1bdb60bd04792b0ee82bb1c53ad5d6
Author: lijewski <mjlijewski@lbl.gov>
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 f27aab14022907461677c075fada9f2ea3c4c3a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 818df3051bc4ab0421de15c9003e5d2c7a27ab46
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e9f844b534edfd960515e9f04dbe169a1d238bae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Dec 4 10:12:21 2012 -0800

    Fix typo

Tools/Release/release.py

commit 41a8bbe9cff4f0a263b13c57bda2e503dbe450cc
Author: vince <vebeckner@lbl.gov>
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 2c84c1ef211d4c05992c03baf5794e97842ee879
Merge: a4dc848 44d38ec
Author: Matthew Emmett <memmett@gmail.com>
Date:   Sat Dec 1 08:47:21 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a4dc8483a2313ab284527a0581e5fc1f3dd71cf6
Author: Matthew Emmett <memmett@gmail.com>
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 44d38ec20c90d225a48e519231d22e2cda2cf8f3
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 27 17:36:11 2012 -0800

    update to the i/o benchmark.

Tests/IOBenchmark/IOTestDriver.cpp

commit 42298f4470b094f00b83522d1b1d67116c48d1af
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 27 17:31:54 2012 -0800

    tweaked the profiling output.

Src/C_BaseLib/Profiler.cpp

commit 08c58fb991636f4cb1429267e9b585dfcf1bcc16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bad069d2dca50387a454aa731477d798920c7f55
Merge: 0fb9bb7 176048b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 27 12:20:42 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0fb9bb794d25acdc85013284f794bdcccc12a070
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 176048bfb80ed2671228a928aea4d4a34e55983d
Author: lijewski <mjlijewski@lbl.gov>
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 2bfde03f60b6008d27c56a1c4d675172fbc9c13c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 862e9c003196570bc8d7c458bd3749407a740204
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Nov 25 10:01:03 2012 -0800

    Cleaned up version.

Src/C_AMRLib/Particles.H

commit d84bb130a610bc238dde54bf0cfa743b5f8ca08c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 10:41:19 2012 -0800

    Fix a bug in my last commit.

Src/F_BaseLib/multifab_f.f90

commit 3a1cddac41d49225e16e84fb02ad33fa10bb7c23
Merge: 5fa641b 403dc58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 21 10:32:12 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5fa641b09ab39f3d6d53b343db97fa7a16c71171
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 403dc58d09ef3dc3cb843eb64f138485d89e1f74
Merge: b120697 2965e36
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 20 17:27:51 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b120697275f4d92590c56eacbb0890877266ed3a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Nov 20 17:27:37 2012 -0800

    Add new access functions in Particles.H

Src/C_AMRLib/Particles.H

commit 2965e36e1cb2b823dfe9602dd73a164cf1ba43cb
Author: vince <vebeckner@lbl.gov>
Date:   Tue Nov 20 15:43:59 2012 -0800

    moved readme to docs.

Docs/Readme.profiling
Src/C_BaseLib/Readme.profiling

commit bb7cae32ca175a758d59265983ae189f03646514
Author: vince <vebeckner@lbl.gov>
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 b2854e00727e1bf278f0db67ba26a6e06a8b19fb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Nov 16 15:16:45 2012 -0800

    Add GetParticleVelocities routine.

Src/C_AMRLib/Particles.H

commit 07fc698cf652b54f7b571a9190f29bde33853ec8
Author: Ann Almgren <asalmgren@lbl.gov>
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 77ce5827a7448ccb367ef9a44ad6bcc25c8ffaa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 9fcaacbd11507f6b6672643d50713077e34621dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dc56abe8bb5763c84a2b65a9c6553bea169b026a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bb1213402966fee5240ef862a7f55eca632c2c43
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 55707a2a6b780b3f2d6654461f1c20f145f16ab8.

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 55707a2a6b780b3f2d6654461f1c20f145f16ab8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 98d886cd0add4eb020f2a84aaacecce6a1702553
Merge: 7549250 4e974a3
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 8 17:25:26 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7549250e2d28be2cd9bf23d983d966561392b6ad
Author: vince <vebeckner@lbl.gov>
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 4e974a3d736013b001ed359313aa258ba6986fa1
Merge: 6aaa576 8f81bf7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 17:12:06 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6aaa576578c424583116d1561b922068c93b0e26
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8f81bf74c3c142c08e11cc42083271c9e55713ca
Merge: 8aef5f0 98eef29
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Nov 8 17:55:56 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8aef5f06cc2ac9fb3501cf9fed60d533260b76aa
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 98eef297062d4e0bc07b0e4908fa5c601849bd5a
Author: vince <vebeckner@lbl.gov>
Date:   Thu Nov 8 14:24:34 2012 -0800

    added some profiling.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/Profiler.H

commit c93c0b1065a4a8110db8c2e5fcb405a701d0b6a4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 8 14:11:31 2012 -0800

    nonblocking fill boundary: do mpi_test

Src/F_BaseLib/multifab_f.f90

commit 85168fa29ad74d96d4743183f3339876063138b3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 7 13:11:37 2012 -0800

    Explicitly disallow copy assignment operator for ParmParse.

Src/C_BaseLib/ParmParse.H

commit f44d013d976025179430ab61aeb6eae8a2869a16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 11:29:12 2012 -0800

    Fix call to isend to make Cray happy

Src/F_BaseLib/multifab_f.f90

commit 9803f50a660d1b4cc2e69b93261dee12d8b38108
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 7 10:54:48 2012 -0800

    fine tune nonblocking fill_boundary

Src/F_BaseLib/multifab_f.f90

commit dcdcfc54cd7f8d578698ef00c35e007b4507a7bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Nov 6 16:59:01 2012 -0800

    Add nonblocking multifab_fill_boundary

Src/F_BaseLib/multifab_f.f90

commit 2fdb906d48933e29d188ab8236b3ee14fa84cc98
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a3bbcece30ea9ae5a33a0fd53a2608472b21e67c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 22:41:23 2012 -0700

    minor improvement of the new fill_boundary

Src/F_BaseLib/layout.f90

commit b3194b061f9531f2394a736137401f873a6aae41
Merge: b771dd3 4753652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 2 22:31:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b771dd30b61072e97073200436e1261ca7bc7e0d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 47536525a1037944b540488d38badc5cf6e55d62
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 2 22:08:06 2012 -0700

    added author list so we can officially be referenced

Docs/UsersGuide.tex

commit 149b8aab0ff270824c4c121b7b70f63d26331544
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7ab073796b12b7c70959bcd1dddd017663b0174e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 60abfa31fc1778cc9d6cc6775ca2207cc949f6e4
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Nov 2 14:47:53 2012 -0400

    enforce string length limits by truncation

Tools/F_scripts/makebuildinfo.py

commit 44a4919a6a0d6f5bb04402c22d90366c24a1d2e3
Author: Marc Day <MSDay@lbl.gov>
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 3562373fcd0290128e4301d86747668d3cc36b8b
Author: Marc Day <MSDay@lbl.gov>
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 6f95081df559193d0ad5d700bb175fe43e4f35cf
Author: Marc Day <MSDay@lbl.gov>
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 55698a7d74bc7fe27df963f0e496a8899b791321
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 29 19:31:04 2012 -0700

    slightly better PETSc run parameters

Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file

commit 68534f7199b167dbf3bf071ea60f52e59c72c87d
Merge: f226be5 a895aaf
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 29 19:02:24 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f226be5ff64e4d5c0ca6bb2b7788f2d653992d82
Author: Marc Day <MSDay@lbl.gov>
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 a895aaff28dde29a8a3f449445bef6ca9718c98a
Author: Ann Almgren <asalmgren@lbl.gov>
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 cd208aabe89ec9c7ee6fd52e18c3898da836571e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 26 06:38:35 2012 -0700

    Only call MPI_Gather if BL_MPI is defined.

Src/C_AMRLib/Particles.H

commit 3630d6c2fcbb4793282c541c4ea034e1ab90df12
Merge: e0e06b0 88947b7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 25 15:23:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e0e06b010fc01c4c5739edeef1f8748fc186649f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Oct 25 15:23:13 2012 -0700

    Make the GetParticleLocationsAndMass new routine work in parallel.

Src/C_AMRLib/Particles.H

commit 88947b7daa00bdd22158c0b517c5c2a2b8f48fe4
Merge: 36f60c1 5dc34a5
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Oct 25 13:58:44 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 36f60c1717320872343ed9b294ddb8b40277269c
Author: Marc Day <MSDay@lbl.gov>
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 5dc34a5c01473dc2b915add2909ea4a23b92eafa
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 523a9b64b8ca94640116185ff61f811d8c966f7d
Merge: 633771f f01b501
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Oct 24 19:54:05 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 633771fa718c9a9515767ea65d73740eadb99dac
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Oct 24 19:53:44 2012 -0400

    add ability to specify min/max for second plot

python_plotfile/plotsinglevar.py

commit a62f48c19058f27cdca5dfb2a6feca98b2b14e5a
Merge: 3de93be 72b8d1f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 24 15:39:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3de93be49f72dcd8768ba7bab9718a95613c518e
Author: Ann Almgren <asalmgren@lbl.gov>
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 72b8d1fd391bc3f2851f2c66626e75857c0d0487
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Wed Oct 24 16:36:43 2012 -0400

    build_hash -> build_git_hash

Tools/F_scripts/makebuildinfo.py

commit 15fce1bad1d55af0d35c3be91aeec39f7426f9a4
Author: Michael Zingale <zingale@localhost.localdomain>
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 bb48d2abf9fc8d5fce806b872c77ad5f5094f2f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 22 17:09:19 2012 -0700

    print more information

Tools/RegressionTesting/reg_test_blame.py

commit 2451eeedc7df7a4258d4ae73bc15f2b7c1391952
Author: Marc Day <MSDay@lbl.gov>
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 73bad4eea0de4676ca32fa4fb75519e3983f9808
Merge: cb47758 1a1cf7f
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Oct 19 14:13:10 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1a1cf7fc929ef709a03bb5c38f8ed4eac80ff5b1
Author: Marc Day <MSDay@lbl.gov>
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 b31818f69ce51ed4359d27570f2746de2b8ff4be
Author: Marc Day <MSDay@lbl.gov>
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 f01b5017462a99dce622997026140e19a945c552
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Oct 17 17:58:58 2012 -0400

    get this compiling again

tutorial/GNUmakefile

commit cb477586fe791c4491b5ed7acf132ae2a6cdb994
Merge: 4615318 5f13721
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Oct 15 13:49:59 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5f13721f7e2a98ac68df3c5bd63944ee74223885
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sun Oct 14 17:46:21 2012 -0400

    some formatting, add builddir if useExtraBuildDir is 1

Tools/RegressionTesting/testnew.py

commit ae3b6b7668346b7f241e3452f4d4968193a04823
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 cf2ea64368a4f3e09f8a69a06dd4cb87b4a2ebbf
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 c4e1eab8b871595ab5035cdd9bb1f5e3ff662c0c
Merge: 635c998 adf3950
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Oct 11 14:53:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 635c998e4b08479d6c1d82ba3b296dc3c25e5c72
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 adf39508954dcf6a011fca7b48b36d0707a33fd8
Author: ajnonaka <AJNonaka@lbl.gov>
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 18c96d7b14538a2ac534a5e1e2782bd0d5988004
Author: lijewski <mjlijewski@lbl.gov>
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 7ebf60c4da91a2a085952519ed191ab0dc79b313
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 10 15:47:42 2012 -0700

    Tweak to OpenMP to quiet helgrind.

Src/C_BaseLib/SPECIALIZE_3D.F

commit f2becbdbb33526edf023dcd9712cace418b65b2d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f2eec7deb0fcdfcacca8ff9f77e1d5176fa31be
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e353ee3b4ed5f3e9eaab8da3a6edca98fd996d13
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 36b64a5745676a87b8956d7ff8e884d5ae562fe1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 12:38:30 2012 -0700

    Fix a bug in make_build_info2

Tools/F_scripts/make_build_info2

commit b4865c43aa0f63525ffee42693b600722b17be9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e77bdca0d5a4d2f63d2d1466188867f7d86c1821
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 9 11:11:27 2012 -0700

    clean up reg_test_blame.py

Tools/RegressionTesting/reg_test_blame.py

commit 078bc10bda40e16c2590c35c6b3e3ad5776b12a6
Author: Marc Day <MSDay@lbl.gov>
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 b6504b1d52485f0b67dcded8ba210cb453cf7dae
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 295824c0acd3b40cfbe7cee1595eadb8e800fc72
Merge: 9af27fe 67c13e4
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Oct 5 12:35:29 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 9af27fe6f9efd5908c247026fc3cea66b04eca66
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 d0a06ad96e08709dcc3c169304512b7d48f176dd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 21:38:42 2012 -0700

    Releasing tool: Fix the taget repo.

Tools/Release/release.py

commit 38f4fde25f183b8f2ad2ec8e66cc6134f3345cfe
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Oct 3 17:43:05 2012 -0700

    Public releasing tool.

Tools/Release/ppCleanup.py
Tools/Release/release.py

commit e826fc0c65bb73306a9841037d15bd9004b801d3
Author: Ann Almgren <asalmgren@lbl.gov>
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 206ca4dc175255591c29ac25a83d70bbaaf435e6
Merge: 22cce50 c9596eb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 3 12:31:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 22cce5059c289999c76e0534617c7fc7821d93d2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 3 12:31:25 2012 -0700

    Get this compiling again.

Tests/F_BaseLib/t_main.f90

commit c9596ebfba6a06922f640d2fde0d4ed0f1809106
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5b61067f069b3032e983d7c751a813982c8de83e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 1 12:23:05 2012 -0700

    Fixed typos.

Src/F_BaseLib/multifab_f.f90

commit 67c13e4febc7c1fe4e13a64f36af6d30bf53163b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Oct 1 10:35:04 2012 -0700

    fcompare: Fix 2D case

fcompare.f90

commit 5c3318dbfc8eba4f37b7105dc2d19e349104750c
Author: lijewski <mjlijewski@lbl.gov>
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 bf485bad689443ee498a82cdc72a6a14b473bfa5
Merge: d7e702c e3f5d52
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sun Sep 30 21:25:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit e3f5d5260e3d16d2ee3fdf512531092c53750b58
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Sep 29 12:53:49 2012 -0400

    not supported

fIDLdump.f90
fIDLdump3d.f90

commit 97ee63b49be67f1f21d191a38723793356a049f3
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Sat Sep 29 11:34:40 2012 -0400

    add NaN detection

fcompare.f90

commit 6ae50ec4b8999ebccf06910b052d5106ebaeabc1
Author: lijewski <mjlijewski@lbl.gov>
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 103f9221620e2b9b313d36255ed88ee49ed0d391
Author: ajnonaka <AJNonaka@lbl.gov>
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 a38e1e57fbc0d4bba0361d75594c78cd3db00daf
Author: ajnonaka <AJNonaka@lbl.gov>
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 f87f6cc08c2e83c00593406614ae9aa8d0e37671
Author: Ann Almgren <asalmgren@lbl.gov>
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 a1512d7749fc01b40b517d5655700a3772bcd9e2
Author: Ann Almgren <asalmgren@lbl.gov>
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 2f45661a202a3cb8499745adcb488ef3741d93be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 24 12:16:34 2012 -0700

    Updated Nyx regression testing.

Tools/RegressionTesting/Nyx-tests.ini

commit 82492c0c8c868bb72e05f4aa142bfba05052c7c0
Author: Ann Almgren <asalmgren@lbl.gov>
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 1d7759d242ad7ba44b42753e4127b45d60001b20
Author: Ann Almgren <asalmgren@lbl.gov>
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 d43cf734365b3b1d79a0f61b8d467d8e31f4e6b3
Author: Ann Almgren <asalmgren@lbl.gov>
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 b8eb9e11c9f8acc88091a478c9cbc989fc659725
Author: Matthew Emmett <memmett@gmail.com>
Date:   Mon Sep 24 12:41:59 2012 -0400

    PyBoxLib: Simplify utils.

Src/Python/pyboxlib/utils.py

commit 2d9e04d12316fbe84b1b47ef3fe97e0c46e6aa2e
Author: Ann Almgren <asalmgren@lbl.gov>
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 d2486309cfda64c682ba637b37a8c901855629c0
Author: Ann Almgren <asalmgren@lbl.gov>
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 65bcfb2f557fff9277eaeb60b95eda430252a531
Merge: 807d572 6adb2be
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 21 17:41:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 807d5724786858611ae94fa6f88a245c11c049e6
Author: Ann Almgren <asalmgren@lbl.gov>
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 6adb2be206611f86a70232cc3a402a77d17d34bc
Merge: dd7183f 6ff592e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 21 16:35:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6ff592e75ead229fd254639f9fb02bb59c144800
Merge: 591216f 1eb933a
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 16:32:36 2012 -0700

    Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib

commit 591216ffc08ef48326451fcab7144aac9e1207a5
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 16:32:22 2012 -0700

    hanlde ifndef blocks properly

Tools/ppCleanup/ppCleanup.py

commit dd7183f77e7023b5c3027b29525e0a2297e9127a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1eb933a5f47c7ef7784c1d723eeb4f549c82be43
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 3aae27d2cd217a512f92d55830c9fad66d06cb70
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 11:48:21 2012 -0700

    I *think* this is working for the pathological nested cases

Tools/ppCleanup/ppCleanup.py

commit a574b8499b891decfa2e6f1fd865f8bc85a76612
Author: cmalone <malone@ucolick.org>
Date:   Fri Sep 21 11:17:16 2012 -0700

    fix character eating with -o option

Tools/ppCleanup/ppCleanup.py

commit 3fe289704ba6c6b5c63cf2c2ceed7bbef3c55010
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Sep 20 19:49:44 2012 -0700

    no longer need to have version 2.7.X

Tools/ppCleanup/README

commit 7a9aa6c18c3b1558eb35f1366f0973f74fdd76ea
Author: Chris Malone <malone@ucolick.org>
Date:   Thu Sep 20 19:44:27 2012 -0700

    workaround for versions less than 2.7 arg parsing

Tools/ppCleanup/ppCleanup.py

commit 4e60f3f0dcc6638cd765b39866ec6bee8e2b6b72
Author: Ann Almgren <asalmgren@lbl.gov>
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 a2f6a971683f34ae28a62ebc82b60f5c3063b5f5
Author: Marc Day <MSDay@lbl.gov>
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 d151cf266235dc90016112078d6a83275059a77c
Author: Michael Zingale <zingale@localhost.localdomain>
Date:   Tue Sep 18 18:12:08 2012 -0400

    forgot to commit this originally

Src/F_BaseLib/bl_prof_backtrace.f90

commit a472cd430b4991780e88d95dd28848d0c3a0fbb7
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 370462023534c3c8fcf0d5d90fdfc283369531da
Author: Matthew Emmett <memmett@gmail.com>
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 d7e702c1db21065e95b02114adf76400b0c50e9d
Merge: f2bc68c 0f55a56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 17 13:50:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit fe6bce435144b207b2dab9039dd8edd2f076bfb0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 17 13:49:06 2012 -0700

    Include <ParmParse.H>

Tutorials/AMR_Advection_C/Source/ADR.cpp

commit c3222db34dff6db5584f0aae7c4215a83fc3a6e7
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 17 13:39:33 2012 -0700

    Fix GNUmakefile in AMR_Advection_C Tutorial.

Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile

commit 71fb05e0091c29d634a7beaff5361262c7bc1750
Author: Ann Almgren <asalmgren@lbl.gov>
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 49834d80a40af1910b7b93300a9e1b9fde64629d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 17 09:57:21 2012 -0700

    Protect against divide by zero in diagonalization.

Src/LinearSolvers/F_MG/itsol.f90

commit 4e5ffc6a84d436ed1d84235a09d5d0f1d34a923d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 14 18:03:57 2012 -0700

    Fix C_Src part of regression testing script

Tools/RegressionTesting/testnew.py

commit d2ed1e7bfd9f754a443e1e5aa96f6b1a2bdd4872
Author: vince <vebeckner@lbl.gov>
Date:   Fri Sep 14 16:31:16 2012 -0700

    instrumented the unoptimized hypterm.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90

commit 3646103599c5dfe8b60f5b2640a6c6ba070dc80c
Merge: 78ab421 161684d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 14 09:37:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 161684dce8fd960f98097bf868cac22fc67b74e4
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Sep 14 11:06:35 2012 -0400

    latest Maestro tests

Tools/RegressionTesting/Maestro-tests.ini

commit bd6d8106a47209846289fca4b0a6a65b864ae423
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Sep 14 10:54:20 2012 -0400

    add support for debug tests

Tools/RegressionTesting/testnew.py

commit 78ab4218b7d8a2181035bee009b86809200e02af
Merge: 9a07ac2 f5510f3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 20:44:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9a07ac2ff0131a87da450c5f2c805a8ee8e0535b
Author: lijewski <mjlijewski@lbl.gov>
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 8be7a7de07c9a19304620a746f680454e5195cbe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:48:01 2012 -0700

    Merged in copyFromMem().

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Geometry.H

commit 35e69b94b09eb6a4139044db57eb6cd795ac94c6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 19:47:25 2012 -0700

    Added copyFromMem() to complement copyToMem().

Src/C_BaseLib/BaseFab.H

commit 0cdfecbf8598b526a2779c5f4222ab618e0b1497
Author: lijewski <mjlijewski@lbl.gov>
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 c64f29148b14b52bf0ab5000baecc12706ca5afc
Author: lijewski <mjlijewski@lbl.gov>
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 26c596c3e3f9aae9966ed4ad325ae38965e5a16d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 13 17:31:53 2012 -0700

    Added static BaseFab<T>::MemCopy().  Specialized version of copy() that
    goes from a FAB to a raw T* memory location.

Src/C_BaseLib/BaseFab.H

commit f5510f3f3290339fd6c44837fd485f3070050605
Merge: 2a17d8e adcc657
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Sep 13 15:00:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2a17d8e23dddece3d5ac45cc9fdd37c5c347a855
Author: ajnonaka <AJNonaka@lbl.gov>
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 adcc65729baf6fd8b946941e29bc5c550734d0b3
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:41:09 2012 -0400

    PyBoxLib: Remove (empty) utils.

Src/Python/pyboxlib/fabutils.py

commit 6ccf72e2ec132787a6d5acaf347e022b5a8a8093
Author: Matthew Emmett <memmett@gmail.com>
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 19bbd5d2c2aa7599a214651d49104ffb2fc2090f
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 16:35:39 2012 -0400

    PyBoxLib: Try again...

Src/Python/pyboxlib/pybl.py

commit 4f43bb2272961df90ed04050d74073c47ed5d5ca
Author: Matthew Emmett <memmett@gmail.com>
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 fdce994c0068cdd40e9c8d7245a95f7d5a89023f
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 13:57:54 2012 -0400

    PyBoxLib: Add fabutils.py.

Src/Python/pyboxlib/fabutils.py

commit 2d3d1f53537d7d8ddbd4031bf815059ee1b5f4db
Author: ajnonaka <AJNonaka@lbl.gov>
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 0c454a3f67808f88bc5ad4ad78e5e107165a9c28
Author: vince <vebeckner@lbl.gov>
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 8f059468bb5a4423d1c40bfe2bb629930982edef
Author: Matthew Emmett <memmett@gmail.com>
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 4fc121b9cd8e374d2b8f10d595b642e17ddb2fcb
Merge: 5d47eec c4b5b52
Author: Matthew Emmett <memmett@gmail.com>
Date:   Thu Sep 13 11:23:15 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c4b5b52ff4e0a18227e1c84256cd2cf05ec0ff2c
Merge: 41b1322 489d7b4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 14:23:13 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 41b13226621a178aa49d678904cf242480d00e61
Author: ajnonaka <AJNonaka@lbl.gov>
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 489d7b42bc0eef58c66ce0c94f319b12bcab84f3
Author: Marc Day <MSDay@lbl.gov>
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 212f8f156afc7699de85402ae4fa43909a4b2fb7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 11:55:07 2012 -0700

    Try again to fix cmake

Src/F_BaseLib/CMakeLists.txt

commit 523406e5c3780ff925d5c71b33020b26d94ca65e
Author: Marc Day <MSDay@lbl.gov>
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 b1488a5b005bd1e82e760301481d30dada8412c8
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 11:19:20 2012 -0700

    update CMakeLists file in F_Baselib

Src/F_BaseLib/CMakeLists.txt

commit 5d2c480548495f6dee61746faf7fed0379341a3f
Merge: 2b39e82 0f3cd3c
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 10:48:42 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2b39e82a091e933071480ad9420c4e266b971c84
Author: Marc Day <MSDay@lbl.gov>
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 0f3cd3c34a74dd338eff36368ea6ec11e6929a2d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Sep 12 10:29:57 2012 -0700

    more cleanup in preparation for EXASCALE

Src/F_BaseLib/define_bc_tower.f90

commit 93ba9f77c413f6e3d0f1f2e73e3996a1c5853873
Merge: af236db c9019d7
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 10:07:37 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c9019d717c819d9ad3ecd0a080171d3dfd7d5442
Author: ajnonaka <AJNonaka@lbl.gov>
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 af236db04fece752fbc79c1104afe229728efc05
Merge: 1f274a3 0ebed90
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 12 08:35:55 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0ebed90306706557d54e2412096c57f6041d1d1e
Author: ajnonaka <AJNonaka@lbl.gov>
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 57e627c47032587b21b1492abb3de93bcdab8d69
Author: Michael Zingale <zingale@localhost.localdomain>
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 41aa4a2a4ddc748b25dad548049caae6a7be80c8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Sep 11 14:48:06 2012 -0700

    local/global indexing bugfix

Src/LinearSolvers/F_MG/cc_stencil.f90

commit fb65b6a7e50ab0efcd4cf8e69ab28ac18315f2ba
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 11 12:39:30 2012 -0700

    A little cleanup.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 5d47eece82aacd4db41c2b25a7a71e14bc1d102c
Merge: 76f9615 0ce350b
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 11 15:30:53 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 76f96159d9ee2eb3a6a8a52741e3c6f6bb371564
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Sep 11 15:30:39 2012 -0400

    MODDEP: Ignore iso_c_binding module.

Tools/F_scripts/moddep.pl

commit 0ce350b3251c701990140f1306b2345e77147818
Merge: d2a3e8b da51c72
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 11 12:09:37 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d2a3e8bfa627efe1bda158603dc156c6c71c1e3b
Author: lijewski <mjlijewski@lbl.gov>
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 da51c729748b41d03214e62d857723dcf6ecb40b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 11 11:00:51 2012 -0700

    Add README file for new Tutorial example.

Tutorials/AMR_Advection_C/README

commit b7ef7da0571010c03152959da6f165c0c14aa8df
Merge: dc66a9b 1c70749
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 11 10:57:55 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit dc66a9b08436015d0efd1503576365700846f3fa
Author: Ann Almgren <asalmgren@lbl.gov>
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 1c70749b56e3b2b86c306cd73655c371757c70fa
Author: ajnonaka <AJNonaka@lbl.gov>
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 f44830cb349a52bf20eba449331500c2ad2ccb79
Author: lijewski <mjlijewski@lbl.gov>
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 642c4efa898678f798776ab66fcd97b0f2a46401
Merge: 5b60c2d 8edbafb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 17:54:42 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8edbafb963c6df2145bbbe2aa16f7514d17f5eb6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 17:06:16 2012 -0700

    fix lall option of multifab_volume

Src/F_BaseLib/multifab_f.f90

commit 5b60c2dce1252287d6e1b7a175f77708559d2a98
Merge: 375cf06 462516a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 10 16:16:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 462516a523d528dc75f8cdee0ffc56a739e8e6a9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8cf1e5fb330b680be473864108b9bb6fae780afb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 375cf06aa8bd5b573bf478c375f2771f9fa37b42
Author: lijewski <mjlijewski@lbl.gov>
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 aa57279710b4fd994a529e8af6aed2f131beb4ac
Author: ajnonaka <AJNonaka@lbl.gov>
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 fc284c8bfa7f2e98ae806afff3f4ce10a6c13765
Merge: 20a4316 39c3c52
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Sep 10 14:42:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 20a4316c32b63c91497c6ce3bca9774d5ee5f97e
Author: ajnonaka <AJNonaka@lbl.gov>
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 39c3c52911535138579f0a223e6cc44649517bd9
Author: lijewski <mjlijewski@lbl.gov>
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 f16039ee9bfa10bbea34518410e34cc66a00f8f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 10 13:16:12 2012 -0700

    nboxes => nfabs

Src/F_BaseLib/multifab_physbc.f90
Src/F_BaseLib/tag_boxes.f90

commit 8e9d240cddc5d3c3637db6741556e80d04c4f82b
Author: lijewski <mjlijewski@lbl.gov>
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 0fb26c8a5917b843a86b7c8d22e8858049f34be0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Sep 9 11:38:30 2012 -0700

    Use binary search in local_index().

Src/F_BaseLib/multifab_f.f90

commit 34c025660d6da99fde73caa9f2f45e243e7e8acb
Author: lijewski <mjlijewski@lbl.gov>
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 8de0ec53336559ef646836151330c0d6235f9669
Author: lijewski <mjlijewski@lbl.gov>
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 0dbe1a85d2e945408ea7ca9cf6f79cd1a99681fd
Author: lijewski <mjlijewski@lbl.gov>
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 39d66168565dcd5f340e3450e3270df41abc3901
Author: lijewski <mjlijewski@lbl.gov>
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 50139d44c5734a6b24ec82d5438b0177ad594dd2
Author: lijewski <mjlijewski@lbl.gov>
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 3b64db8eedf585ff278b706ec3c79afd72c7713c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Sep 8 09:42:48 2012 -0700

    Merged in local_index().

Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit aa422d65e033b20d5e9951f90f4faa8bc24c77e2
Author: lijewski <mjlijewski@lbl.gov>
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 b018d5e0815b00a795d46169202da28752629459
Author: lijewski <mjlijewski@lbl.gov>
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 e4b5b771898f29bed5b27b5e81c91fb36fbb1df4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 16:35:26 2012 -0700

    Tweak to local_index().

Src/F_BaseLib/multifab_f.f90

commit 76507d4a9ef430a5f181d760e98c42e1027ac2ca
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 16:23:03 2012 -0700

    Merged in local_index() calls.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 53ee2c6cfa6969ee2beae2b554c274a75069590b
Author: lijewski <mjlijewski@lbl.gov>
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 0addc281775d97532dd9e28defc7de5351aba8f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 13:02:09 2012 -0700

    get_[ip]*box() work on local indices.

Src/F_BaseLib/multifab_f.f90

commit 2b6cf463e9b0226ed9eaae462da9cc4e7203750f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Sep 7 10:41:33 2012 -0700

    Merged in local_index().

Src/F_BaseLib/multifab_f.f90

commit 1e9555362ecb84772bd1ce304578c84dd850b94f
Author: lijewski <mjlijewski@lbl.gov>
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 c5d624fd047e7e831cdfdae3f7c58749be80f5b3
Author: lijewski <mjlijewski@lbl.gov>
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 9f31e3d56cfdbdf85c20108f2826ff748d0993e9
Author: lijewski <mjlijewski@lbl.gov>
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 b83d8a83eb9b66b0b96f6c4ce295f5763c5fd4bb
Author: lijewski <mjlijewski@lbl.gov>
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 7631189eeeb80fcc883aeeb2e13a869636951ce6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 6 12:52:27 2012 -0700

    Reverted out an ill-advised numcomp -> ncomp substitution.

Src/C_AMRLib/FluxRegister.cpp

commit 28e51281ae5996cbf23dbdf74b3607aed79748ed
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 22fee0ed185bac9fc2a74c0a3919cc4ae76b0f69
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 65e664aa2adc33f41627c737214653012efabf1f
Author: lijewski <mjlijewski@lbl.gov>
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 c257fadfdf260401996ec7eb83a7b2cc831a739e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 5 09:02:51 2012 -0700

    Pulled some computation out of an inner loop.

Src/C_AMRLib/FluxRegister.cpp

commit 99d8b31c0ed87fd92613c37dcef51dc2bb42888b
Merge: 0748ce8 663b15a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 4 15:01:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0748ce818c1ff1cf2d1c4629c35cb84a4b8368cb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 4 15:00:48 2012 -0700

    Simplified mapPeriodic() a bit.

Src/C_AMRLib/TagBox.cpp

commit 663b15af1bdf212d21cd887b5fc63733fe36f6cc
Author: Ann Almgren <asalmgren@lbl.gov>
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 b381d3a5a7df159baf7f9974feaaae5cf179324c
Author: lijewski <mjlijewski@lbl.gov>
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 f8c45d71cc0a9f7dc2b43c90fc60cd99ca746fe9
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 5a8ab4ed62bacce67b1a3405ce5bbbe9f7fd9e8e
Merge: db8d650 bb5877d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 13:39:43 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bb5877daff8b52d51ef6b663b645bf42aa7133ad
Author: vince <vebeckner@lbl.gov>
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 db8d6509de52acdfa651d155b5b75132bc16ff7c
Author: lijewski <mjlijewski@lbl.gov>
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 ee6c6a3f49cfcf5826fc30d55bc07256eb5c31ef
Merge: 9daf040 d61ca59
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 10:56:28 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9daf040ffedc5b911eeb2c812d5988e3b436f01d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 31 10:53:45 2012 -0700

    Have Finalize() flush cache.

Src/C_BaseLib/DistributionMapping.cpp

commit d61ca5996086d8b102c11270d82a192bedc1fca6
Author: vince <vebeckner@lbl.gov>
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 0cf31ca5e3c2664656876da44a2b3b0750cb3e17
Author: lijewski <mjlijewski@lbl.gov>
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 fdcb53499139e24b8a09cfecf3e0254e4fd42632
Author: lijewski <mjlijewski@lbl.gov>
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 65ae89dc229cb00fe3be3e131d63446601dd0ed5
Author: vince <vebeckner@lbl.gov>
Date:   Thu Aug 30 13:23:58 2012 -0700

    added openmp flag for c.

Tools/C_mk/Make.defs

commit 697740dbf7002eefc4a965dd31c9f13fc92b9056
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 16:13:28 2012 -0700

    undid some changes from hopper.

Tools/C_mk/Make.defs

commit 608e45fe54da0c95a5d3f91afb60481f186e2cdf
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 16:07:07 2012 -0700

    set omp flag for regular c.

Tools/C_mk/Make.defs

commit 85810c15b0fbcb5b146178d49364bb8e54c04b6a
Author: vince <vebeckner@lbl.gov>
Date:   Wed Aug 29 15:54:22 2012 -0700

    omp fix.

Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F

commit 2415e3a5c58fd52b9dc64bfedb29bfd6f33d9f69
Author: vince <vebeckner@lbl.gov>
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 d4dd2a3344eaedeca54e96a22f59bf527a580960
Author: vince <vebeckner@lbl.gov>
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 ea17ff7b5499c20856237b628a22f0abf2faea81
Author: lijewski <mjlijewski@lbl.gov>
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 9660f8dbabf6309a923f2abe0443d6c7cd634466
Author: lijewski <mjlijewski@lbl.gov>
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 b9bfc3147a81cd139eb52b818394766c9eeb0805
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:28:29 2012 -0700

    Little code cleanup.

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryRegister.H

commit cd944109d88ff9d0ec335ac71ee0dc0e61f86956
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 29 10:13:03 2012 -0700

    Simpler (but equally good) key calculation for copy cache.

Src/C_BaseLib/FabArray.cpp

commit dfc463e761f322f5f251830b2cf0a00b7be6af38
Author: lijewski <mjlijewski@lbl.gov>
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 f3a9feacfb7a2f10a81a411d127dfcbe8643ca50
Author: lijewski <mjlijewski@lbl.gov>
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 5f3c8e0f9482b167ed873aaf306a6687c1da0968
Merge: bbd68ca dbeb697
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 28 16:49:25 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bbd68cac40e9b3089268d6d28468c19cdb9d35fe
Author: lijewski <mjlijewski@lbl.gov>
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 dbeb69737ad80ea4b8a914e1e361862a740733ab
Author: vince <vebeckner@lbl.gov>
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/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/README

commit ad20735aaf6ed4e862e96a3247e4262c97b0e125
Author: vince <vebeckner@lbl.gov>
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 96893aca1b7d5c39a523487d738fbbfe750c7b75
Author: lijewski <mjlijewski@lbl.gov>
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 bee39c643e93617b82efefb0b80cae74b10e3731
Author: lijewski <mjlijewski@lbl.gov>
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 9e314edf7da121b21f3f056dbefe8e8dc0c6c749
Author: lijewski <mjlijewski@lbl.gov>
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 bc7e450453c5a1415e6eb2ea4bf036d388600466
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 16:56:02 2012 -0700

    Increase max size of FillPeriodicBoundary() cache.

Src/C_BaseLib/Geometry.cpp

commit da7bd02eb73b507609609ac8424fac0d32f84d3c
Merge: 9a5f685 12a6981
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 16:44:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9a5f6853ede15333fe422afb21f14145b0f97845
Author: lijewski <mjlijewski@lbl.gov>
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 12a69810b330ea1bd276f118fa510cd28ad5ae33
Author: vince <vebeckner@lbl.gov>
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 90fbd81e6e9215c5a13761c29dedfe979336b446
Author: lijewski <mjlijewski@lbl.gov>
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 5044d9a87fd13723c4583f3bd1b9739e68fda7e2
Author: lijewski <mjlijewski@lbl.gov>
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 d9b89f4e7b4fc77ce430eeeabbc5b87c212712b9
Author: lijewski <mjlijewski@lbl.gov>
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 1b336fcdee6e06cf99396d47e5f14fc5a65d53b5
Merge: fe909fa 1344340
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 27 12:18:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 134434043da61fab2419a45455a7109a137f74ba
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Aug 27 10:59:42 2012 -0700

    Fix a bug in getRecentFileName in regression testing python script

Tools/RegressionTesting/testnew.py

commit fe909fa3790d2654c79f129ed43dfcf1c0035c58
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 13:52:48 2012 -0700

    Call FabSet::Cache() on regrid of level 0.

Src/C_AMRLib/Amr.cpp

commit 982a5b125dfba7f06615b86beabf5260dfabb021
Author: lijewski <mjlijewski@lbl.gov>
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 a1b1950d9de0ada605a90e4b22df054875033d82
Author: lijewski <mjlijewski@lbl.gov>
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 c5d0f7b22773764d163041f19b08f6ba17ad68ce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 09:55:55 2012 -0700

    Simplified Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit 6cfa536b68cee797e48fe95b6e0404f3443106f1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Aug 26 09:21:48 2012 -0700

    Simplified CrseInit().  Removed CrseInitDoit().

Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/FluxRegister.cpp

commit bdf8ba1f5284730750bc236068266634e2ba81a8
Author: lijewski <mjlijewski@lbl.gov>
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 e894a538e79881caba9032e82ed6b290e28c895e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 25 19:11:41 2012 -0700

    Yet more code consolidation.

Src/C_BaseLib/FabArray.H

commit 58a30f1e74ca08b699ebf88a9bd6857b76d3c197
Author: lijewski <mjlijewski@lbl.gov>
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 4b9fb43a75545f680c3caa0a1e67cafbd8d2ba26
Author: lijewski <mjlijewski@lbl.gov>
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 512e849b796864c5a02da2a938c5c2cac7e5ff06
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 22:14:40 2012 -0700

    Didn't have some logic quite right.

Src/C_BoundaryLib/BndryData.cpp

commit fac4245df4a6265f25319ce5d80ee8059c53d58e
Author: lijewski <mjlijewski@lbl.gov>
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 87e3bcf2000c53ee32ab8a92f2024a4a8a9f69c6
Author: lijewski <mjlijewski@lbl.gov>
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 1cbe403f621105d296800365b135e68a0717a11b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 16:53:39 2012 -0700

    Removed some #if 0 code.

Src/C_BaseLib/FabArray.cpp

commit 74e470a62623f65f1134ea26a312039e66155ca2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 16:46:45 2012 -0700

    Minor performance mod to periodicShift().

Src/C_BaseLib/Geometry.cpp

commit f4b1a5c6bb8862390f659672d850853697dc7dcf
Author: lijewski <mjlijewski@lbl.gov>
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 e8a4941f216050f1057eeae16abaec494a127627
Author: lijewski <mjlijewski@lbl.gov>
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 84de73bc1a6e502528f061bf6524c2ec5e961277
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 24 13:30:35 2012 -0700

    A little more refinement.

Src/C_AMRLib/FluxRegister.cpp

commit 474e3eac259eff15adee2f36c0e18293400f3bd1
Author: lijewski <mjlijewski@lbl.gov>
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 e4b62153fd090963a8c536a4a378a4114d2d5b03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 23 17:35:59 2012 -0700

    Further simplification.

Src/C_AMRLib/FluxRegister.cpp

commit 2190d260217d7a4754b2290e74f9100bc0f7ce32
Author: lijewski <mjlijewski@lbl.gov>
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 4e29d28d9908392627aeeb214fd7bd64ac1c2b30
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 23 13:21:04 2012 -0700

    Very modest simplification of Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit afe8c4375bf392f61fff5a48d0afba531454ee01
Author: lijewski <mjlijewski@lbl.gov>
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 7ecb281614b9e92cb5a59c480a736e82a35169f2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 15:35:51 2012 -0700

    Regularized some typedefs.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 84a88dd336c2a7317e505dfbdeaa6b8f65d6d055
Author: lijewski <mjlijewski@lbl.gov>
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 0e3c3405bfc971a3223e01e150b0997d4eb3b5f1
Author: vince <vebeckner@lbl.gov>
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 ebeb824a82a32cccac719495874211da22d529cc
Author: vince <vebeckner@lbl.gov>
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 a4384cd1dc176b68c1ee7a5c1e3146641ee0daf6
Author: lijewski <mjlijewski@lbl.gov>
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 d8298cef94146005c1c72252c97170ddad741c3e
Author: lijewski <mjlijewski@lbl.gov>
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 f48114e2dfe2f5be1608c770f449c2e289e37e50
Author: lijewski <mjlijewski@lbl.gov>
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 f8a03a63dd8b741fa6302d0bed8bbeeebcffc426
Author: lijewski <mjlijewski@lbl.gov>
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 283edce059ee20673f1319995eb6d1cb34575eb1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 09:37:16 2012 -0700

    Handcoded optimized parallel routine for SumPeriodicBoundary().

Src/C_BaseLib/Geometry.cpp

commit 68e92ee8b5724e85cf7730e26a3664fa70dbf071
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 22 08:28:49 2012 -0700

    Fixed compilation bug when !BL_USE_MPI.

Src/C_BaseLib/FabArray.cpp

commit 06d28dd3b7ea01657f512d874ac8d0f0dc4c816c
Author: lijewski <mjlijewski@lbl.gov>
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 bc7bec94c6ed333a1b65550dedbe3b6c1b0d7f0c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 19:30:31 2012 -0700

    Removed SIRec structure -- no longer used.

Src/C_BaseLib/FabArray.H

commit ae6d0770113a469f3342a1f668eaae3e7af436e8
Author: lijewski <mjlijewski@lbl.gov>
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 5437e22a487d3ed50d6883dd2a81fb8b7fd7e8f1
Author: lijewski <mjlijewski@lbl.gov>
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 e6d8f05b61584ac85ae05db500545e81aba11466
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 16:38:05 2012 -0700

    Handcoded parallel routine for SumBoundary().

Src/C_BaseLib/MultiFab.cpp

commit f374de43061bcd1afb6c1fc9c93c41a76c13b4dc
Merge: 2dcae23 1cfb636
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 16:37:45 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1cfb636fb07ca37d7013a1367b0940ce13a8eaed
Author: vince <vebeckner@lbl.gov>
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 ff8da35a597965a27e6ba5048e226ac763808de6
Author: vince <vebeckner@lbl.gov>
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 2dcae2309c63304b39b37c68854e67c735d523af
Author: lijewski <mjlijewski@lbl.gov>
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 21b85f0b9527ae8c80f47ed84541d8d3bd20b929
Author: Ann Almgren <asalmgren@lbl.gov>
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 a61dded61450a388103a97a01adc2ef72b4f472a
Merge: 5001097 a532724
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 21 10:48:26 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5001097001846cac63c4513758d39687c02f24f7
Author: lijewski <mjlijewski@lbl.gov>
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 af1d6eecf18369d575411862e3e3e46d2c1fb496
Author: lijewski <mjlijewski@lbl.gov>
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 a53272407108fcc6262c044f2fd416add7898b48
Author: ajnonaka <AJNonaka@lbl.gov>
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 ff5c1a139420efe03fd6f07d0f0d9be3d2214070
Author: lijewski <mjlijewski@lbl.gov>
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 76500feff119ab12182d1462eee05a16329ee45e
Author: lijewski <mjlijewski@lbl.gov>
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 bda454d14bc7007227bf58efec782c371dff5be5
Author: lijewski <mjlijewski@lbl.gov>
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 458ae45d4cbfd5578eece227789ea33775289d86
Author: lijewski <mjlijewski@lbl.gov>
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 2620d1cda8ea4cba9918190bcdcd44cd53c97b2f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Aug 20 13:08:27 2012 -0700

    Final Final.

Src/C_BaseLib/FabArray.cpp
Src/C_BaseLib/Geometry.cpp

commit 7f4464187ad3a6190b98274ac8d74b2929580ddd
Author: lijewski <mjlijewski@lbl.gov>
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 ca9e852d6b95d162d7861b21a7f3b162ff67a309
Author: lijewski <mjlijewski@lbl.gov>
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 0555e55f23b955db2e8a4e5c92f9f85fc058b4d0
Author: lijewski <mjlijewski@lbl.gov>
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 2d349fa8dbed6a61de79b5b18e1f2413f8d680e3
Author: lijewski <mjlijewski@lbl.gov>
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 7de611daa00173e1430072ffd09e5e6fe5a5c868
Author: lijewski <mjlijewski@lbl.gov>
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 91dd7ebd4ac8a7b1d803b911bc16afc3fe850255
Author: lijewski <mjlijewski@lbl.gov>
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 063d49ba0dc24f3a46a974a761af3651b1223694
Author: lijewski <mjlijewski@lbl.gov>
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 8e71f085275e3f30bbe44e7604194bd4ec78f327
Author: lijewski <mjlijewski@lbl.gov>
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 9084a8cd286328e619d6af895958bc566315ee64
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 18:40:11 2012 -0700

    Inlined FabComTag constructor.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 41e29aabb23c42b8f482989a8dbba471309a2953
Author: lijewski <mjlijewski@lbl.gov>
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 9b00519a794faca3295ba86ce31728688b660b17
Author: lijewski <mjlijewski@lbl.gov>
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 2021aeff6453c1e06bd5a7707245e05d0a657496
Author: lijewski <mjlijewski@lbl.gov>
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 b9e83dfcd58b05a6aedbc44d8134f10f6a246815
Author: lijewski <mjlijewski@lbl.gov>
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 5f7b31b13296c39efc512203df9c7f96a9137593
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Aug 18 09:13:33 2012 -0700

    Untemplatized TheFPB().

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 743fc1ec2af883982f2b2629c17ff029b1c1c516
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 16:26:05 2012 -0700

    A little more error checking of input cache sizes.

Src/C_BaseLib/FabArray.cpp

commit d445c0712d8b80c1da07583d5c564e27b25b8014
Author: lijewski <mjlijewski@lbl.gov>
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 074c3407cfa5819e213cb0fde98193c056fdbc26
Author: lijewski <mjlijewski@lbl.gov>
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 64ad3bc7856e613ba9d258db83218b13df36fb78
Merge: 6c1615c 3b41737
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 17 13:56:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6c1615c344bb015313990dbc516fb55d60d62815
Author: lijewski <mjlijewski@lbl.gov>
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 a0a342913e74ec8e5258a5cd8737d14580cec749
Author: lijewski <mjlijewski@lbl.gov>
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 3b41737ee90450b2f1597088428a7c0db9087c36
Merge: 5a09635 a26a96e
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 17 13:22:53 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5a096355d4d659176ed65b292e1192456ff6c0a6
Author: vince <vebeckner@lbl.gov>
Date:   Fri Aug 17 13:22:23 2012 -0700

    gnu.

Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit a26a96e512693d2021b63ab2c52f0bb0f368cbef
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 df398fd8484023c97ca324a6df40937d54d7697e
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 f6ff299b7c0c24a2a7528e531bfeddcaa471b4c6
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 ba285bd39cede4a841a36756020142e526d1953e
Author: lijewski <mjlijewski@lbl.gov>
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 9cd023f2cd6a0c717bc9884b6ebd4793ad99ca9b
Author: lijewski <mjlijewski@lbl.gov>
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 e4fb985a8c6c12df7256658ae65a95d902118b0e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 18:03:10 2012 -0700

    More tweaks to CollectData().

Src/C_BaseLib/FabArray.H

commit d3219ab6ac872ff588501e9423f85d032d72954d
Merge: 419146f bf7c2e4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 14:47:02 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 419146ff6cc7df89c1401c40f778655cda2a3e92
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 14:46:49 2012 -0700

    Squished out more memory from CollectData().

Src/C_BaseLib/FabArray.H

commit 92d311cb511ff447f3653c2cda30cf7197a19f6d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 13:03:21 2012 -0700

    Removed unused variable.

Src/C_BaseLib/FabArray.cpp

commit bf7c2e46f87a2442495ac3ef54bf394df5f85c4f
Author: Ann Almgren <asalmgren@lbl.gov>
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 04ceb6cc3a02070fd0ff942bd234576afe27ecf5
Author: lijewski <mjlijewski@lbl.gov>
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 a0de0205e7d523f466f314cc0b0da6f0672ac6a0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Aug 16 10:04:00 2012 -0700

    Changed the send count cache used by FillBoundary & FillPeriodicBoundary()
    from an Array<int> to std::map<int,int>.  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 fecebcc120f1ead7e6bc7dd4bf6e82d4627d629c
Merge: 1a90437 d2588c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 16:23:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d2588c3f5fdcad47e1afde09c836ea4bdb0c249c
Author: lijewski <mjlijewski@lbl.gov>
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 1a90437f7904e234245bfb1116a3a5c499addbd5
Merge: dd9138b e3f54c6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 10:37:31 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit dd9138b6235b6c30892c1a268804bf48d7e9df32
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 14 10:37:18 2012 -0700

    Fix a comment

Tools/RegressionTesting/testnew.py

commit e3f54c6ee6f004a2427051ab392e60406e28481d
Merge: 84e0716 9553fce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 14 09:35:59 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 84e0716de61eb51e78e8e1171dc7f064619ccb3b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 14 09:11:08 2012 -0700

    Set verbose to false.

Src/C_AMRLib/AuxBoundaryData.cpp

commit 9553fce6cfbf721efae915ac4a198d8c0ef434ea
Author: Matthew Emmett <memmett@gmail.com>
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 16402f204b94cbc95fcac6838b295eee8b61b557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 21856cb8e95fd3afaa5f6caa5c9a54d527a2dbef
Author: Matthew Emmett <memmett@gmail.com>
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 2f36539e319d2576dc760c1671f9856c10a9701d
Author: Matthew Emmett <memmett@gmail.com>
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 0f55a568964aa1d1aca4d8ac540c634e74fa5fc8
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Aug 8 21:10:40 2012 -0400

    some minor fixes (deallocates, comments)

python_plotfile/fsnapshot.f90

commit 40a2ea134d6f194dfe717beba0a076f143472036
Author: Matthew Emmett <memmett@gmail.com>
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 ff14d31f3716358a1d6bda8a1aebba27bada56ed
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 a4ed93f696f2373068527dc5a2e27594fc029781
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 8 14:37:34 2012 -0400

    add methods to get at the variable names

python_plotfile/fsnapshot.f90

commit 8085200159435601f063a7f98b3b1828cf82fb51
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Aug 8 12:48:08 2012 -0400

    add support for 1d data, for flame plotting

python_plotfile/fsnapshot.f90

commit dbb7011c6b5acf96ef2aba2a825feb49b37ed21f
Author: lijewski <mjlijewski@lbl.gov>
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 e7c430257585f6a7f3145156bdf93e81225f07b6
Author: lijewski <mjlijewski@lbl.gov>
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 8f3613052005f1cd7583036c4c366487520338bc
Merge: e81f651 7f8d823
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 7 18:50:39 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7f8d82365722e524fad6caea903adc19f311c42e
Merge: ca6fa36 974aeb1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 7 17:28:04 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ca6fa36e1a107b1b8d0cbafc9b9283b5fee4d1e1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Aug 7 17:27:53 2012 -0700

    Increase the precision of numbers written to Header

Src/F_BaseLib/fabio.f90

commit e81f65100bc4a73bdef2f47ba55d21102e70bdc6
Author: lijewski <mjlijewski@lbl.gov>
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 974aeb1ba65bcd68aede07ae99fb5317173ba2e0
Merge: 676abbd a9a3ebc
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 7 10:13:10 2012 -0400

    Merge branch 'chemotaxis'

commit a9a3ebcd5c2a588f7cedc008bdf9041a4856e956
Author: Matthew Emmett <memmett@gmail.com>
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 676abbddd21c429182bf578b2f6a1cda2546eddf
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Aug 7 10:12:21 2012 -0400

    PyBoxLib: Bug fix.

Src/Python/pyboxlib/fab.py

commit 3dd46fda1fbe8924198c9143fb2b4432fac2ba06
Author: cmalone <malone@ucolick.org>
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 155901569aaa141fd287a8495a82f969cb21f2b5
Merge: 6d0c685 194a911
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Aug 4 20:52:32 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 194a91136df5ff3e80a630f8771adf3204c47a1f
Author: lijewski <mjlijewski@lbl.gov>
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 6d0c685edfa51ef346097b193a5ed148754592ca
Merge: 3c4e9b8 12fc2bf
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Aug 3 10:49:19 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 12fc2bf4cc45a108b37b378f38eb8840f9ffcdf1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 3 10:41:58 2012 -0700

    revert

Src/F_BaseLib/define_bc_tower.f90

commit 3ce2731d0f5afed02d938b352a6e14a6265284b1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 3 10:41:15 2012 -0700

    revert

Src/F_BaseLib/fabio.f90

commit 3c4e9b8dded9f232b879744f9745832c71562140
Merge: 23e4588 8e83122
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Aug 2 21:16:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 23e45889755e4d53ff4d70334ec53496e5d185cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 25b835afc7135fe2722fb4ec82875a426eaf09d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8e8312285bf8d22bfd86f252871c7ff909728795
Merge: d8b422f 6c86a20
Author: Sandra May <smay@lbl.gov>
Date:   Thu Aug 2 16:51:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d8b422f030f432e2580f8f2cfdb65f469f1f895c
Author: Sandra May <smay@lbl.gov>
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 6c86a20dad2e24792ec2b865eeddce4f0aa0691f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Aug 2 16:37:51 2012 -0700

    test commit

Tutorials/HeatEquation_EX5_F/main.f90

commit 10f93ea6599b282eae90874ab03bace98806ccbb
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 65ba033fd5fd317f7a4490df539150513555c011
Author: lijewski <mjlijewski@lbl.gov>
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 01a2f314b94fc32060817419c41b883775e097d0
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 d05778a3db3a24e852d63779d2fab72aaed27a39
Merge: 3a56fe7 4853fce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 14:45:31 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3a56fe74698dd58f35554e5f510f8ec0d72678ce
Author: lijewski <mjlijewski@lbl.gov>
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 4853fce34ee366e8eb05896c3e1e80fc4851a059
Merge: 8383125 d8b0dc4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 1 14:36:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8383125bf1ae591d70d92fb337ca681389ebbf57
Author: Ann Almgren <asalmgren@lbl.gov>
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 d8b0dc42419b93d80af56f64dddee27708d929a2
Merge: 4cb851c 255f630
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 13:38:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4cb851c06b4e5a63d39bdfa35fd09d165c1eea33
Author: lijewski <mjlijewski@lbl.gov>
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 764754d2de1ffb18473189dc3ed9088d2c3a1777
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 13:33:55 2012 -0700

    Fixed typo in my previous fix.

Src/C_BoundaryLib/BndryData.cpp

commit f9a4149a80112ecb28e670cad88c1921c79795c1
Author: lijewski <mjlijewski@lbl.gov>
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 ee24b14f3fc3ffbec2f3cd24364357ddd21b5d3b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 1 12:49:57 2012 -0700

    ngrd -> grd in a couple find() functions.

Src/C_BoundaryLib/BndryData.cpp

commit 255f630df95c35eca1e0122367f0a6c6f9b704ff
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 e5abce187a9dddc8e16e297cf0fd041e146c1d16
Merge: c27f9f5 f902913
Author: Sandra May <smay@lbl.gov>
Date:   Wed Aug 1 11:13:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f902913e899922eaf37bda61cee846c3cedbecd9
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Aug 1 11:12:07 2012 -0700

    added an lmultifab_build_edge subroutine

Src/F_BaseLib/multifab_f.f90

commit 57cf699dfcb8d77a911ea615d10931a589056f72
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 0372a100bb7fa586f8cf8660751e68573b5b7daf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 31 19:32:02 2012 -0700

    Had argument order switch.

Src/C_BaseLib/MultiFab.cpp

commit 82d5b68f0d222423365505eea37b6051dcb48591
Author: lijewski <mjlijewski@lbl.gov>
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 6e41c7704b83e792c5a950d17ec3f83bb925a270
Author: lijewski <mjlijewski@lbl.gov>
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 c58cd32ac61fdcb5ebbace68bbf2d49a03c6f751
Author: Matthew Emmett <memmett@gmail.com>
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 c27f9f572cf10cf0ec33cf5ea69aeb6371a61ab3
Merge: dd0d3da 2475496
Author: Sandra May <smay@lbl.gov>
Date:   Tue Jul 31 12:32:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2475496cab253d18e4252b2f3efa624bdb5c6223
Author: Matthew Emmett <memmett@gmail.com>
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 6e008af670a5eeff0e375ea6dc3dae609c0df2a3
Author: Matthew Emmett <memmett@gmail.com>
Date:   Tue Jul 24 10:27:17 2012 -0400

    CHEMOTAXIS: WIP.

Tutorials/Chemotaxis_F/chemotaxis.py

commit 198f2b97dfd94c06621b45c6f6d16a54aa44a22c
Author: Matthew Emmett <memmett@gmail.com>
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 07fd4adb40fc0bb4d8fac27ce82da1b2e8e15d79
Author: Matthew Emmett <memmett@gmail.com>
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 421cce52970f43ae2e942377d969d7e24dedbe1b
Author: Matthew Emmett <memmett@gmail.com>
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 3109955e41a2feae036b3096d0a9b6e2d90153d3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jul 31 11:11:19 2012 -0700

    Add definitions of FLOW, IRRFLOW, etc,

Src/F_BaseLib/cutcells.f90

commit 6a80ffce826f301bac855622c8ab0314bf0ac85d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a226dff884e184e5736fd015da78c6283dc39e05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0fe009c915057d8e0e7a1a0da6b9519c3815b01c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dd0d3dabd606fb39a1b69392e6a59e5341afb009
Merge: e2c8ef9 1dbaf45
Author: Sandra May <smay@lbl.gov>
Date:   Mon Jul 30 10:11:04 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1dbaf45d6b513f42b8d2a9e86a544bcb6e0b8e92
Author: ajnonaka <AJNonaka@lbl.gov>
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 9c59dcef9a18775b36616c78ba302c50f8ab4604
Merge: e5fc8be 506891d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jul 28 21:12:32 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e5fc8be6980ebd10715e2631920d80b529b932dd
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 506891d3a9b84f918f6f945606a887ddf67f6302
Author: Ann Almgren <asalmgren@lbl.gov>
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 8f248c6509bac594cf13ba2da1272ddc1a55aeb8
Merge: 90b4e61 d508b85
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Sat Jul 28 07:28:39 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 90b4e61059aa1dd640361bbc4545fdc531295ba5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d508b85e2ad94e02cd50ca963654c54fbe9d8b06
Author: Ann Almgren <asalmgren@lbl.gov>
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 e509176939f9d0b4f44c0abeea44ece271852227
Author: Ann Almgren <asalmgren@lbl.gov>
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 c797c028961361e93103acbf7c46811e26863a05
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 27 17:04:22 2012 -0700

    minor update of usage string

Tools/RegressionTesting/testnew.py

commit d2833df779bbab7f20ac53eff64758c49b24b43b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2155c62e324f10c95fc2aea2c7a793e995e8df72
Author: Ann Almgren <asalmgren@lbl.gov>
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 e449ae53559ebdde0f4eae3bafc3bdeaff34357c
Author: Ann Almgren <asalmgren@lbl.gov>
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 c3b8c05694c96c196442d8c11991329d8986e9f1
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jul 27 11:48:16 2012 -0700

    added debug checks for varnames.

Src/Extern/amrdata/AmrData.cpp

commit f0d4b6dd14bb106f0a062a2056493dfe851b9df0
Merge: 260be6e 7eaf3b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 27 08:42:49 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 260be6ef4bba8911b79623158fa727913589efc3
Author: lijewski <mjlijewski@lbl.gov>
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 7eaf3b82c9dffa87d5b01106a70f62994beb4cad
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jul 26 22:38:47 2012 -0400

    really fix it now...

Tools/F_scripts/make_build_info

commit 9c6aaa8b51340faa9371e8a11683f553757a1476
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jul 26 22:37:49 2012 -0400

    fix compilation

Tools/F_scripts/make_build_info

commit ac7138adb4bdd5334fed703a11889af96ea318ec
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 b8d4b7d41c410c9a6629d5880a4b0fb439b6487d
Author: Regression Tester account <regtester@battra.(none)>
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 c4ae93e6296cf380dc7fe6a43c0a1715f3de5978
Author: Regression Tester account <regtester@battra.(none)>
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 54499346dfcc5b42e9a2b2d1bcac7eeec8057c49
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dfa27bad3fd6836f3fa95d65adfcfb584ab76a01
Author: lijewski <mjlijewski@lbl.gov>
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 d48102247e916f17a9aac369d50eb1cdca45927f
Author: Regression Tester account <regtester@battra.(none)>
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 bf27bd82de2d3bd5aa7b8efe6d0c2233e2930cd0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 681838b19f2deaa80f8841dfbf652888909df95b
Author: Ann Almgren <asalmgren@lbl.gov>
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 ca1b5620f7b75e775f7aa68793a18baeabaf1832
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 409ab742fd987dcb7ffd07d68a3e3dd756288d9d
Author: Matthew Emmett <memmett@gmail.com>
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 10d9e991d15f10039cf4a2b38b10b11f6ddc1cf6
Author: Matthew Emmett <memmett@gmail.com>
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 79421977cb522ac051e971d98ae1d3f3500cd7ee
Merge: 00c6723 735ba41
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jul 23 21:35:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 00c67237ce704ea29b19ae737549a4b0fe62c3c2
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jul 23 21:35:01 2012 -0400

    fix a comment in the mg_tower options

Tutorials/HeatEquation_EX5_F/advance.f90

commit 735ba4138422472fdeec2b020c9a2289320cbbbe
Merge: b9b222b 9e57e62
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jul 23 18:23:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9e57e62d2ded550fbf2884abf22cc0394e8a4da6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 16:33:15 2012 -0700

    Using the new BoxArray::const_iterator.

Src/C_BoundaryLib/FabSet.cpp

commit e4d012f70eaef2bcc03af2aa63ceddb431035306
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 16:32:18 2012 -0700

    Using the new BoxArray::const_iterator.

Src/C_BaseLib/DistributionMapping.cpp

commit 3855aeb038b186aaa9957f90d7056ae9edcb7c5a
Author: lijewski <mjlijewski@lbl.gov>
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 b9b222b250f7fc7dd4a1e314d9209553c402afd5
Merge: 7cfd2c8 8447560
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 20 14:51:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 844756022516a895ad9f8a4e7ae1e4afe4088dee
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 20 14:45:51 2012 -0700

    Used iterators more extensively.

Src/C_AMRLib/AmrLevel.cpp

commit 7cfd2c8512317a4e19ee40d901649c714016fea9
Merge: 14951ed b4b3171
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 07:05:01 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 14951ed07c84624d548e259f7326220325540ea4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jul 19 07:04:54 2012 -0700

    Add baragon to F_mk

Tools/F_mk/GMakeMPI.mak

commit b4b31715e87c220d3bb0af91c44e892d4ee48ebf
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 ece0088b47e135b79730ba1f441e65755762bdec
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 24e2115656336e236c3d0df9a09c31236021ee7c
Merge: 5e06064 680388f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Jul 18 19:41:17 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5e06064ddea9f7fc8727c54df8e18e24d669e190
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 680388f6cfb0685017ed76767d60dba60e7a70a4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 16:13:53 2012 -0700

    Just a minor tweak.

Src/C_BaseLib/FabArray.H

commit 1b583c3354e7904384a2ba57a7ac1dbff7620c2d
Author: lijewski <mjlijewski@lbl.gov>
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 b2e44f706e688910d56c091b7c982adb6729d59b
Merge: 1ce42ec b738028
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 18 12:14:10 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1ce42ec7464481c3095ab8645a41e23b977396de
Author: lijewski <mjlijewski@lbl.gov>
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 46153187fee8e7781665384e90ffafd1f4ca7606
Merge: d2081ba b738028
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 18 12:02:43 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d2081ba761281e5af88cd77d1a6f901b14d63132
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jul 18 12:02:33 2012 -0700

    need quadmath on Marcs laptop

Tools/C_mk/Make.Darwin

commit b7380282315f4b89731d65899e348c9e5e3151c1
Author: Michael Zingale <zingale@jaguarpf-login2.ccs.ornl.gov>
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 1f274a353cbd2a5280eadf086a15cd508d6fd93f
Merge: 4ce6439 3e41457
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 22:57:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3e414575a3e7f15258b22ca4ffa4098a0bdafcfa
Author: lijewski <mjlijewski@lbl.gov>
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 08cf2346b9d479c5193faaaf2e26338aacd5d277
Author: lijewski <mjlijewski@lbl.gov>
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 9aa3885857775898420cdb3953abd8cec3a64284
Merge: 67709ec 6b4dc6b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 17 13:26:24 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 67709eceb4cc20e0f877c68369d723e21b26ee79
Author: lijewski <mjlijewski@lbl.gov>
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 4ce64396757951c36e9a9aa07e6c46ca6c33c217
Merge: a4c3068 6b4dc6b
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:24:24 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit a4c3068c945251532939fbfb0632136130244318
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:23:39 2012 -0700

    add TagBox include file

Tools/C_util/ViewMF/viewMF.cpp

commit b23a99c43bf47b55684c1e172748f12cc0d67e41
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Jul 17 11:23:07 2012 -0700

    Add special rules for hedorah

Tools/F_mk/GMakeMPI.mak

commit 6b4dc6b91d9d78dba0bce85b3beef5af692ad221
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 940bde4c962e1a7e95d83d34370cb461c695aca2
Merge: 63860b2 c4ef4db
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jul 17 08:34:41 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 63860b2e7b69b246dc0cd8fc1e2390b6872d42fb
Author: ajnonaka <AJNonaka@lbl.gov>
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 c4ef4db23c377e416e51b4ddc8729f8d48cabda0
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 0af64ddb08e75990510a02ab8e49ae5cd8529904
Author: lijewski <mjlijewski@lbl.gov>
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 9c2c1e1ca30954b3074afe9e7c15322ecfa256d6
Author: lijewski <mjlijewski@lbl.gov>
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 710799820a92f0031f7d816ab4c787405382e1c1
Author: lijewski <mjlijewski@lbl.gov>
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 a5f102f7c8ff75e21a13c9dd258902e5bb15f511
Author: lijewski <mjlijewski@lbl.gov>
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 2fe86a29f0ce2237051ef761952e2f7a92a28192
Author: lijewski <mjlijewski@lbl.gov>
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 b1736020e8f04d9ea987b45e0a358ef545852d46
Author: lijewski <mjlijewski@lbl.gov>
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 29decf7ab90769748c00795bd544bca2887acfe7
Author: lijewski <mjlijewski@lbl.gov>
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 c38b71b494ed1d92cb4d41d60b49f6afd42bdde5
Merge: e925dac 5451cac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 13:26:44 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e925dac7456fc03614925c22ccca31d2ae86ea9d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 13:25:11 2012 -0700

    minor updated

Tools/RegressionTesting/testnew.py

commit 5451cac3fc9977e70fe8196b126ab8346c7a5310
Merge: 64c530d c3be672
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 13:01:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 64c530daefbf59fd2b74373df55d4c126bee2a66
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 13 13:00:00 2012 -0700

    In BndryData changed the following member data:
    
        PArray<Mask> masks[2*BL_SPACEDIM];
    to
        std::map<int,MaskTuple> masks;
    
    Also, changed the following member function:
    
        const PArray<Mask>& bndryMasks (const Orientation& face) const;
    to
        const MaskTuple& bndryMasks (int igrid) const;
    
    using to the following typedef:
    
        typedef Tuple<Mask*,2*BL_SPACEDIM> MaskTuple;
    
    In MCLinOp.H, changed the following member data:
    
        Array< Array< Array< Mask*> > > maskvals;
    to
        Array< std::map<int,MaskTuple> > 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 c3be672d72cdd420ccf653cc9a1712fd2e8bfbb5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 12:59:05 2012 -0700

    another bug

Tools/RegressionTesting/testnew.py

commit 4a932e09719e52ccfac04248af37a7bb501db071
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jul 13 12:43:22 2012 -0700

    fix bug

Tools/RegressionTesting/testnew.py

commit 8195cddf7ee146fc407686fe38e7d54086c3af74
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5a2790b09389d1ac37991432425da78b80dd8d87
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e2c8ef9137a70e5f0137bc1a8a876c5b7dcd04f8
Author: Sandra May <smay@lbl.gov>
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 0d281aca286e5c831b1e5c5871b37adfb839a2a9
Merge: 1c01e0e 30327b8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 14:29:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 1c01e0e7157a4baf1293e25f4dbfe7cf49c306de
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 14:27:57 2012 -0700

    Prototype of BndryData::bndryConds() changed from
    
      const Array<BoundCond>& bndryConds (const Orientation& face, int igrid) const;
    
    to
    
      const Array< Array<BoundCond> >& 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 88a8631bea8525a4d8e2f8a79e8ace4ba9bd26aa
Author: lijewski <mjlijewski@lbl.gov>
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<Real,2*BL_SPACEDIM> RealTuple;

Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryData.cpp
Src/LinearSolvers/C_CellMG/LinOp.cpp
Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit f0b33579a19cf13c16cb7022aafa327c1760741e
Author: lijewski <mjlijewski@lbl.gov>
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 30327b84e6d8e976722c7c76d8f39c0ce5b3fb15
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jul 12 12:43:00 2012 -0700

    changed default.  this is not used anymore.

Src/C_BaseLib/VisMF.H

commit 1819262972e0081a7c90fb9f2766b8d3899a7c70
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 12:37:41 2012 -0700

    Used std::map<int,RealTuple> for bcloc instead of
    Array<std::map<int,Real>> 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 ed4b766b06a98a79799bf83337cb51325eebd2f8
Merge: 7728eb4 3febd03
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 11:00:07 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7728eb416d54f24db3a355dffaf83da6d508b04c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 10:59:01 2012 -0700

    To further cut memory overhead, maskvals & lmaskvals use a
    Tuple<Mask*,2*BL_SPACEDIM> instead of Array<Mask*> for each grid they own.

Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/LinOp.cpp

commit e1a83ee8f6df15fba22b9fe6880dda67417a36d1
Author: lijewski <mjlijewski@lbl.gov>
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 026761eedf5b521b8ea56f74369247e3bc5448eb
Author: Sandra May <smay@lbl.gov>
Date:   Thu Jul 12 09:59:22 2012 -0700

    added integer parameter to define FLOW, SOLID, IRRFLOW

Src/F_BaseLib/cutcells.f90

commit 8c8e392e44d53f6dc68e23cf99626c61f864f392
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jul 12 09:22:27 2012 -0700

    Replaced some uses of std::vector<bool> with Array<int>.  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 3febd0391250f4245ffc86827d2fc636a82a5c29
Author: Matthew Emmett <memmett@gmail.com>
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
Src/Python/src/boxlib_numpy.f90
Src/Python/src/boxlib_numpy_c.c
Src/Python/src/boxlib_numpy_f.f90
Src/Python/src/fboxlib.f90
Src/Python/test.py
Src/Python/write.py

commit 3a467dd828971e5b2831ad227c7643ae6bde1d85
Merge: 3b10a0f d0142db
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jul 11 21:33:46 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3b10a0f28b21bc4949a7eb43c3412125e6104e0c
Author: Matthew Emmett <memmett@gmail.com>
Date:   Wed Jul 11 21:33:27 2012 -0400

    PyBoxLib: Use boxlib_initialize instead of parallel_initialize.

Src/Python/src/fboxlib.f90

commit d0142db51e748e39a6c4c2325a39d776afdb7c7c
Merge: 74438db 59dc8f3
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jul 11 18:18:55 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 59dc8f31b8cfe0812ac69f34997c4aef52dd9c8f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 16:46:21 2012 -0700

    In BndryData, change the following member data:
    
        Array<Real> bcloc[2*BL_SPACEDIM];
    to
        std::map<int,Real> bcloc[2*BL_SPACEDIM];
    
    Changed the following member function:
    
        const Array<Real>& BndryData::bndryLocs (const Orientation& _face) const
    to
        const Array<Real>& 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 14455d20c2121cc85f28690a4b53c4c26d506df3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 15:56:42 2012 -0700

    In BndryData, change the following member data:
    
        Array< Array<BoundCond> > bcond[2*BL_SPACEDIM];
    to
        std::map< Array<BoundCond> > bcond[2*BL_SPACEDIM];
    
    Changed the following member function:
    
        const Array< Array<BoundCond> >& bndryConds (const Orientation& face) const;
    to
        const Array<BoundCond>& 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 74438db39a7aa65ce1372b303d34e968eb8e7c9c
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jul 11 14:57:07 2012 -0700

    Fixed PList pop.

Src/C_BaseLib/PList.H

commit 5b326422ef0d2e5347e1090cbbbb5d1337f5679a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 14:16:22 2012 -0700

    Got rid of the following data member in StateData.cpp:
    
      Array< Array<BCRec> > bc;
    
    Got rid of the member function:
    
      Array<BCRec>& 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 726e11e50af42f32b30d4836fcc9f9328f6b6ef1
Author: Ethan Van Andel <evanandel@lbl.gov>
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 4b2f5d3e0a78c1dd925d712e354d9f4e46073107
Author: lijewski <mjlijewski@lbl.gov>
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 851402278e750eb7cac441a6a9164720f0a1363c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jul 11 09:13:34 2012 -0700

    A little simplification.

Src/C_AMRLib/AmrLevel.cpp

commit 506365e743dcba8bbfbae124142656370f51c99e
Author: Sandra May <smay@lbl.gov>
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 a6b7285babb244db8e2ed4e8580e3c886bcd6dc3
Author: lijewski <mjlijewski@lbl.gov>
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 757b99ec5bec2618052ff386dce1512d1ff6bc86
Author: Sandra May <smay@lbl.gov>
Date:   Tue Jul 10 13:06:54 2012 -0700

    added 2d option

Src/F_BaseLib/cutcells.f90

commit 77ad27235997bf433b1b73ebcd5bae97880ae7ad
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 20:11:26 2012 -0700

    Removed unused variable.

Src/C_BaseLib/FabArray.H

commit 064630d31f450265070b5dbc47ee8c07503ec12c
Merge: c52a043 4035d67
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 23:07:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c52a04326e13d5c8fb6bfc1a0a843a7ea48dbc0e
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 9 23:06:46 2012 -0400

    A little more overlap of computation & communication.

Src/C_BaseLib/FabArray.H

commit 4035d67ebd1a730d8023790c65e993db81ceba8b
Author: vince <vebeckner@lbl.gov>
Date:   Mon Jul 9 16:37:43 2012 -0700

    changed comp to gfortran

Tutorials/Exp_CNS_NoSpec/GNUmakefile

commit 4e13222985d86368e7d66c7962dac5f20da96c37
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 12:17:54 2012 -0700

    Removed debug messages

Src/C_AMRLib/Particles.H

commit 57a1e292f45ad655efe1e0c2cc91f12c094d28b9
Merge: 1d5ceb5 a1869d8
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 11:10:00 2012 -0700

    Merge branch 'master' into hybrid_sub

commit 1d5ceb51d8e20ffec04f1e1c91b63ef11413123d
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jul 9 11:09:11 2012 -0700

    Added finest_level option to AssignDensity

Src/C_AMRLib/Particles.H

commit a1869d8f2acca615c9f87c3f9ec22f358e32acb9
Author: ajnonaka <AJNonaka@lbl.gov>
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 cec7c17b0e90c7d4f6dd62eb4faf853f8cc4da0d
Author: lijewski <mjlijewski@lbl.gov>
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 866079b6b73c73b52bb0c3e4fcbe1925a1a86766
Author: smay <smay@atragon.lbl.gov>
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 93c38d997299ce55140b30bed3ce92c436533320
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jul 6 09:41:14 2012 -0700

    Turn off some uninformative Cray C++ compiler warning messages.

Tools/C_mk/Make.Linux

commit bb6012e6dcc2bf570237b610e571331f4150e570
Author: lijewski <mjlijewski@lbl.gov>
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 f272f5a39b541ae0cb69a819fd0cb180fa9aa684
Author: cmalone <malone@ucolick.org>
Date:   Thu Jul 5 12:41:52 2012 -0700

    file not used in docs

Docs/Preface/preface.tex

commit be71463d98a9aff1179a788784cad14c01293b3f
Merge: 3ee5731 1c8dda4
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Jul 5 16:20:41 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3ee5731335f668a70d318088765c393c92bb740e
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 1c8dda49a12ed9e543975f0c743995998fc81461
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 3 16:15:04 2012 -0700

    added enum back.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 4b1dfd197cb2ffc82781ae57215049789531c315
Author: lijewski <mjlijewski@lbl.gov>
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 32e7f18218a26b69a4c0f8da9a68d194a1a2743e
Author: vince <vebeckner@lbl.gov>
Date:   Tue Jul 3 15:40:43 2012 -0700

    added mf read benchmark.

Tests/IOBenchmark/IOTest.cpp
Tests/IOBenchmark/IOTestDriver.cpp

commit 6799bac447291864a84859848af3595a953ec112
Merge: 9091b7b 34015a8
Author: vince <vince@gigan.lbl.gov>
Date:   Tue Jul 3 14:09:11 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9091b7b6306ec0d4a4c1a58c64495997f0c7a864
Author: vince <vince@gigan.lbl.gov>
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 34015a8f95425debc870ec614c5ba3c1a0ff6893
Merge: 193656b 212361e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 13:59:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 193656bb84ce6c737273b964232167596b5cf40a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 13:58:28 2012 -0700

    Added some more stuff to cutcells.

Src/F_BaseLib/cutcells.f90

commit 212361e7afaa3f611ca60663054f1f5a8b929b19
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 c7c0970a681bd1b5ee8b89e6bad54486d13a81f0
Merge: 51b3289 482c363
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jul 3 15:16:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 482c363dbb53ed838578ccd394ccf3bdc64dbf5d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jul 3 09:52:44 2012 -0700

    Added ParticleContainer<N>::NumberOfParticlesAtLevel().

Src/C_AMRLib/Particles.H

commit 8a7f0a8847fda955cf3dd35c063e9e7b24daf360
Author: lijewski <mjlijewski@lbl.gov>
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 69b92f866c36cf8271ac8da629f647b4c39aaec7
Merge: 94a732e 12d2c40
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Jul 2 12:53:42 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 94a732e034ab6837bb9dc62cb6a14e9cb47283aa
Author: lijewski <mjlijewski@lbl.gov>
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 b84727067af995b7e138c1bcf42cd11fbb143f0c
Author: lijewski <mjlijewski@lbl.gov>
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 12d2c40b79b291c9d8d46ad5ad3974e8e2a3f963
Author: Ethan Van Andel <evanandel@lbl.gov>
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 c1b37c461f9b743b3698ea28a75e6aa12dd12142
Author: lijewski <mjlijewski@lbl.gov>
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 671e628bd313f5832a4e3a844c97ced04df4aa3a
Author: Ann Almgren <asalmgren@lbl.gov>
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 51b32890295fda6ff7d6043e713ad95e2a726fb5
Merge: e705bbd 085a690
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jun 29 20:20:24 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e705bbd2ea3fe59f42bad45f1a2b9c9910115202
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jun 29 20:20:00 2012 -0400

    start merging in some of Weiqun's changes

Tools/RegressionTesting/testnew.py

commit 085a6905b81e4c569775176d6dd5c1f57da311be
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 29 14:37:01 2012 -0700

    addition for ipm gnu

Tools/C_mk/Make.Linux

commit fe4f6b7b461d3b251b1f140364b40df0d10d10df
Author: vince <vebeckner@lbl.gov>
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 308ebd9cffbfbcb38dc6d86ed9231e90a647b041
Merge: f7f7e79 baf1213
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 29 13:57:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit baf1213b8515ce7fb35c18ad270cb39b78c7a71b
Author: lijewski <mjlijewski@lbl.gov>
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 4d6a7def907a9ce6e3959de3aa96de4724b36580
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 13:25:40 2012 -0700

    Defined MPI_DATATYPE_NULL for non-MPI builds.

Src/C_BaseLib/ccse-mpi.H

commit fdd8d8ca8c8f19bd096bb81a3e80684fe4edb37c
Author: lijewski <mjlijewski@lbl.gov>
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 1320e357a4950125856802fad695a9c7fe9d0a2c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 12:51:21 2012 -0700

    Fixed typo.

Src/C_BoundaryLib/FabSet.cpp

commit 58aadfbd96f6c4805c347b64e5c1f2e5f96e8bdb
Author: lijewski <mjlijewski@lbl.gov>
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 8e6c035afcd8958716d62ec5bb4367305543f995
Merge: 7926b53 5fb7f49
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 11:26:46 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7926b533d8f13b41ff2ce136ae24ccbd79a344a3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 11:26:35 2012 -0700

    Removed some redundant code.

Src/C_BaseLib/BoxArray.cpp

commit 5fb7f49a044276a529c56da20103283160ddf68f
Merge: 20f774d 83ff0f0
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 11:19:38 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 20f774de39a8d4dbfaa80b5718a62b84b8601887
Author: Ethan Van Andel <evanandel@lbl.gov>
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 83ff0f00665d2163fd937f4a66aaa24f7855734c
Author: lijewski <mjlijewski@lbl.gov>
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 94a870b3f95d91aebda33c109599eeb1ba5991a2
Author: lijewski <mjlijewski@lbl.gov>
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 4f7ecbb995b75c0f61c31f8c787b416e7170acbf
Merge: 6460cfd 0019957
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:59:09 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 00199574f77ef7f5b0294b10d785789a472eb3de
Merge: e55ba73 c72dade
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 29 09:56:19 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e55ba734e91c3ad01d75abed3eadf6b4cf669c60
Author: Ethan Van Andel <evanandel@lbl.gov>
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 6460cfd292d699b9bb273c0fd31ad119cc63c3c3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:40:47 2012 -0700

    A final bit of polishing.

Src/C_BaseLib/FabArray.H

commit a2b58bc1fa4cb10651c3f9953ebe389e6b7eaba6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 29 09:14:45 2012 -0700

    Inlined & simplified some stuff.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit c72dade6f2ab27bbc78617946102461be3518e4b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 17:37:28 2012 -0700

    Inlined a few things.

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit 735f0a65fe61a3ccbd42518e066d854ea31c3bf3
Author: lijewski <mjlijewski@lbl.gov>
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 8762865b76e89e275867dbe7920d69baa0a8d286
Author: lijewski <mjlijewski@lbl.gov>
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 f2c6f123598e71c82d8b31af8502178ae9cdd6da
Merge: e7792f6 0611d12
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jun 28 15:45:07 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e7792f66c6474899b6fdd62c12ea0f8c762e4cb0
Author: lijewski <mjlijewski@lbl.gov>
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 0611d129125e9010641e44999338f570ffed2e5d
Merge: ecf5281 42bfb42
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 28 15:18:54 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ecf5281b688964044bd36175dbfd02e6698db3b2
Author: Ethan Van Andel <evanandel@lbl.gov>
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 42bfb42097383b288f89c42a83833f20a7ebcbf7
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 38c8af034014f2579dd0ba46c8ce489d1656ea3c
Author: Ethan Van Andel <evanandel@lbl.gov>
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 281cb403cabc567a04ef71efc01a3685e296f28b
Author: lijewski <mjlijewski@lbl.gov>
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 78c1bb984d269c4cba941d1ec010c1f39a7352e5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 27 12:45:11 2012 -0700

    Minor efficiency improvements.

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp

commit 211b113c398b741406734c8db95325cc9c1900fc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jun 27 12:26:46 2012 -0700

    Some memory efficiency improvements.

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit d2023dc690937cfda5c50cc60f197095fca4a97f
Merge: 77441ac cbfca81
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 12:26:06 2012 -0700

    Merge branch 'master' into opt_sub

commit cbfca81cbe47e8dd4a682c5fe78d81acda93f2fb
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 11:28:53 2012 -0700

    One more ADDI fix.

Src/C_AMRLib/Particles.H

commit 0e9299180d9c6799d8cc996b559568efacbb474b
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 11:19:01 2012 -0700

    Level indexing fix for AssignDensityDoIt

Src/C_AMRLib/Particles.H

commit 7de38a20de896c9330002a69129e64c029491190
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:35:41 2012 -0700

    One more small virtual numbering change.

Src/C_AMRLib/Particles.H

commit 369956b112c634241b60f8fa82c72d009cccfedb
Merge: b95fe45 ca54cfc
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:30:56 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b95fe450c1a1df83465da80a8f550d32b9ada59e
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:30:02 2012 -0700

    Fix to AddParticlesAtLevel and virtual/ghost particle numbering.

Src/C_AMRLib/Particles.H

commit 77441ac813d1430f35d96b9887d143982f135e77
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed Jun 27 10:29:24 2012 -0700

    Work on optimal subcycling

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit ca54cfced38fcd48edc4989c1d77fb7911bb49f8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 17:35:57 2012 -0700

    Minor simplification to collate().

Src/C_AMRLib/TagBox.cpp

commit 466074e67491014109414201f1c5cf1e43cbfafe
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 26 17:11:06 2012 -0700

    Some cleanup of minIndex() and maxIndex().

Src/C_BaseLib/MultiFab.cpp

commit 0665a823242cbb895b1dd26e5775ba72ad262903
Author: lijewski <mjlijewski@lbl.gov>
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 5dffbe6563cd52072d936aac27768dce9c76aa55
Author: lijewski <mjlijewski@lbl.gov>
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 76cd743059bda73018935c6918a5ad323020584e
Author: lijewski <mjlijewski@lbl.gov>
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 36ec3340b84b9111d94b5dda238e9c6b7e895cc8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jun 26 13:07:31 2012 -0400

    better way to do the labels

python_plotfile/contourcompare.py

commit 31dd2e32ff5f3623fb16d50364d43967663612c3
Author: lijewski <mjlijewski@lbl.gov>
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 2f109e0688d0efcaa4b333873f5d7a88eaec7ef8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jun 22 09:07:26 2012 -0700

    Cleaned up some warnings.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 4c08f8fe57e63c6a17a5dff022584a7c6a2d53a2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 17:00:42 2012 -0700

    add @echo SUCCESS for regression testing

Tutorials/HeatEquation_EX5_F/GNUmakefile

commit 72b9e066069473a57c3211fa8ccd448951da1b20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jun 21 15:27:25 2012 -0700

    Fix makefile for this tutorial

Tutorials/MultiGrid_C/GNUmakefile

commit d48739a7bcb1a23191b1f555c59ef36a7ede57b8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4001987431545d7fdeab43e2e5de09774c7615d1
Merge: d077aa0 2316c0d
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Jun 21 13:28:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit d077aa09e2d5df22bcb0889e78b5c9137992c138
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 156f23c62daf6f70bce1dd32a0f74c24e49e3ed4
Author: Vince Beckner <vebeckner@lbl.gov>
Date:   Wed Jun 20 16:46:19 2012 -0700

    fix for battra.

Tools/C_mk/Make.mpi

commit 87d976a3d88e3f00f63ff0c0eaaa8ad356c14309
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 20 15:13:10 2012 -0700

    fixed error in makefile documentation

Docs/GettingStarted/GettingStarted.tex

commit ec58b183abfa7d012509d70284e1ae1e31789275
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Jun 20 14:41:52 2012 -0700

    note about makefiles

Docs/GettingStarted/GettingStarted.tex

commit 14f996c077fb4b6f02860556c1c712e27ee9082e
Author: Ethan Van Andel <evanandel@lbl.gov>
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 ef32878b8001d89faa4358d1de4fdaa97966307f
Author: Ann Almgren <asalmgren@lbl.gov>
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 a5ec4a9eda17ccd864d38ea8df4fb9f8ddeb4d2d
Author: Ann Almgren <asalmgren@lbl.gov>
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 c1432d62ee9345eb875316a0a1d9be5b083e568d
Author: Ann Almgren <asalmgren@lbl.gov>
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 5f8d95a8e99bccb0f9bd6590abe5fa6df37a45ba
Author: lijewski <mjlijewski@lbl.gov>
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 4fedde37eaa72171f4ca76d20d02c3ae96579e57
Merge: a900da3 4c467d6
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 14:30:52 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a900da3a625e423619e378f7cddbd59f9ae8c251
Author: lijewski <mjlijewski@lbl.gov>
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 4c467d694b920827b4e8629558d81d94001e4f88
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 13:28:59 2012 -0700

    Fix typo: "ghost" --> "ghosts"

Src/C_AMRLib/Particles.H

commit a7b098d373fe566f5a772d91433602204ef55ce3
Merge: 8909977 c712e3d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Jun 19 13:26:27 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 890997708b51bdaf9205cee5f6ee15e1f72b6fe4
Author: Ann Almgren <asalmgren@lbl.gov>
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 c712e3df482bb9e233a50aec9eae48693b5bc39d
Merge: a79ea80 479499d
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:55:43 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 479499de5f568386334cb15bdd8fca9e1162cb15
Author: lijewski <mjlijewski@lbl.gov>
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 a79ea8030050d6d6623b2c6f4f928ca811edff34
Merge: b594021 255990a
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:37:59 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b594021444e1dac1a410400f33ff6762689be6be
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 15:37:32 2012 -0400

    specify defaults on the declaration line

Tools/F_scripts/write_probin.py

commit 255990a71d7191644fa8e755541aab91051b9bc4
Author: Ethan Van Andel <evanandel@lbl.gov>
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 9d50f09a7b921d53651bc6c4dabcad6d9b1314b0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Jun 19 10:36:44 2012 -0700

    Simplified RemoveParticlesNotAtFinestLevel() & RemoveParticlesAtLevel()
    among other minor tweaks.

Src/C_AMRLib/Particles.H

commit 2316c0d03bb0927fd54ca212970b2204908232ad
Merge: eeeba07 3d038b0
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 13:09:16 2012 -0400

    tweaking of the makefile

commit eeeba07b84fb81f999052f277137171e9a1aa8e1
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jun 19 13:04:27 2012 -0400

    get this compiling again

GNUmakefile

commit ad56e065e47404e08b8d4543c5d7137b3772417a
Author: lijewski <mjlijewski@lbl.gov>
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 7c4b77b2de45bc5351387f1cb19c54e4ebb6f5bb
Author: lijewski <mjlijewski@lbl.gov>
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 32271a1a717c3076a6b84d99fc59f0fbc655d2a5
Author: lijewski <mjlijewski@lbl.gov>
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 dfef3a64d2761f1995a2d1fc1b33975f5885b2f0
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 10:17:26 2012 -0700

    More cleanup

Src/C_AMRLib/Particles.H

commit 32d43a77b48ae662c2746cd94a85794a5e37d04c
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 10:16:21 2012 -0700

    Pre-push cleanup

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/Particles.H

commit a8bef047f312f4ecb038073a71f5aa74113d15fb
Merge: 2050bc8 9fd4023
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 18 09:40:35 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9fd402397ebbb85ec569d83f466295215cbdd1fa
Author: Chris Malone <malone@ucolick.org>
Date:   Fri Jun 15 19:51:48 2012 -0700

    add libquadmath for all gfortran's in Darwin

Tools/C_mk/Make.Darwin

commit 991ead74dd38245f8551d5367cb5c6935717bdd0
Author: Chris Malone <malone@ucolick.org>
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 2050bc829d7df053aa7f1246352b752c1cf4ce83
Author: Ethan Van Andel <evanandel@lbl.gov>
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 247252f1ec29651dfadfda886893bd1c36366c81
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 15 16:56:15 2012 -0700

    Minor additions to subcycling parse logic.

Src/C_AMRLib/Amr.cpp

commit a04f6273c858cc867faca8f3c18dc490c7612c18
Author: Ethan Van Andel <evanandel@lbl.gov>
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 ac7d972332077cf24befbf1a09c7990151dd1d2d
Author: Marc Day <MSDay@lbl.gov>
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 90db26a959bba8caf6dd1efd1dbba96725bff218
Merge: fbe7007 85dca7c
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Jun 15 14:26:50 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fbe700735a3f702d64cab3daef3cc602784ad4f7
Author: Marc Day <MSDay@lbl.gov>
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 85dca7c8828cf6b1591a1c87fbfce917374ec36d
Merge: 74ac690 2d69e7c
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Fri Jun 15 15:57:08 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 74ac6907db42d5079dcfe2c299fef641f64bd2df
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 2d69e7c1e24f76c9104c4860099c922285299398
Author: lijewski <mjlijewski@lbl.gov>
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 ad4a5d57bf9f57011cf6d08b049812a67df1288f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 048d3975b57dbcc7c86a9baf60d1d5d9f74ecdd2
Author: Ethan Van Andel <evanandel@lbl.gov>
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 f7f7e791034729e8891fc805e7ec27bb3ac407ed
Author: vince <vebeckner@lbl.gov>
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 f0bf05782a191e36eb2b17c2dc2a8710e68c0f7c
Merge: f44de40 3d3c778
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Tue Jun 12 13:14:55 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f44de40273502bb530b5a1a7f90ec78caabc082d
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 5552bad167c7559770a9172bc42f252346a39151
Merge: 75601eb 3d3c778
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 11 09:30:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 3d3c77868db4f2212a164246dc8847a6f471d57d
Author: Ann Almgren <asalmgren@lbl.gov>
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 df364a45c4005e0afa07a7949cf28fa8cb121c6d
Merge: ad6841f b7fda4c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Jun 9 15:09:40 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ad6841f9a7786249c1db5b6cde59c03e543efe2b
Author: Ann Almgren <asalmgren@lbl.gov>
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 39f5bd2ee2b8ae8fa53cc5cb070dc8d3c293057b
Author: Ann Almgren <asalmgren@lbl.gov>
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 75601eb0874314596e1b30fabdd2374fff46d8a7
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 8 16:38:32 2012 -0700

    DERP fix.

Src/C_AMRLib/Amr.cpp

commit 1da913a4f2bebb2d86921a3f0cee75f48129d6c4
Author: Ethan Van Andel <evanandel@lbl.gov>
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 0801b25866d51e354a1768877ede86d730545871
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri Jun 8 14:33:04 2012 -0700

    Fixes to subcycling assign density.

Src/C_AMRLib/Particles.H

commit b7fda4c45af930d09428d9d90fdff7ea3a5ead7d
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 10d2f62861d61bc60b79f6e773a08ba55297ff11
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 7 16:23:19 2012 -0700

    Minor fix to periodic ghost cell densities.

Src/C_AMRLib/Particles.H

commit 79818822af9aa1794d10f0a30fbc9e3afc46262f
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Thu Jun 7 11:04:36 2012 -0700

    Debug to nonsybcycling redistribute.

Src/C_AMRLib/Particles.H

commit f3099a1f7b3dcbb626bcfafa3b5ed913c4d6dcfc
Author: Ethan Van Andel <evanandel@lbl.gov>
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 3d038b0e3f595dc14fbb07b102ee371fccaa8b60
Author: Christopher Malone <malone@ucolick.org>
Date:   Thu Jun 7 11:28:44 2012 -0400

    get this working with updated make system

GNUmakefile

commit 5e5bddfa03c675811e56d207304ea90180a7dc17
Merge: 3d76fea 4d37e80
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jun 6 13:20:52 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3d76feafae55967affa1e5c8880430111f68d24a
Author: Marc Day <MSDay@lbl.gov>
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 4d37e80e018b15c7531395c531137c051b1bf4cc
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jun 6 13:08:58 2012 -0700

    init for max and div optimizations.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit ee1282eaf5b0c0f8c6566141ea39e37340373b6d
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue Jun 5 13:01:05 2012 -0700

    One more merge fix.

Src/C_AMRLib/Particles.H

commit cc1ba810715e8dde57c4f96ecc6e8e683244789d
Merge: 59b1100 3b21290
Author: Ethan Van Andel <evanandel@lbl.gov>
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 3b21290aa9d4a376291d042993990f95741829e0
Author: Ann Almgren <asalmgren@lbl.gov>
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 d423bc8da6a0982b48b5845ccdd0a90db0614428
Author: lijewski <mjlijewski@lbl.gov>
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 89d96e9bb2bae63e35dbb68ed60272bc68831afc
Author: ajnonaka <AJNonaka@lbl.gov>
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 24a91d1c5d32cfc4fc0ac940bf8250dde9eb879a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jun 5 07:53:29 2012 -0700

    added subroutine multifab_build_nodal

Src/F_BaseLib/multifab_f.f90

commit 382029737051e5a624f8a35aabb32b47aa23cfdb
Merge: 9989f76 821232f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 20:17:25 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing

commit 59b11008c1fac3267333b4372045d4fe62887d43
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon Jun 4 17:17:03 2012 -0700

    Working Ghost particles, debugs.

Src/C_AMRLib/Particles.H

commit 9989f76d8cc55667308082b1ac3db31b59791e2b
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 20:16:14 2012 -0400

    remove constants and random as packages needed for the build

GNUmakefile

commit cf0b689a9754d76e972377125a1f55b26afcde29
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 c07ad9de070d44784f41a8f6684badd4c892972c
Author: cmalone <malone@ucolick.org>
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 9bf3394ebcb2cfe526bee2ac528d6ed5a2112c1b
Author: cmalone <malone@ucolick.org>
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 ccfab6768d5083ac97922dc99b490b53998aed2f
Merge: 0100830 72f613e
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Jun 4 12:30:03 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0100830406855a381214c419106afe8ebab1817d
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 72f613edbbe1128f592a2fe18f25ece74deb6232
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sun Jun 3 20:56:49 2012 -0400

    add support for AstroDev

Tools/RegressionTesting/Maestro-tests.ini
Tools/RegressionTesting/testnew.py

commit e95043c15996f42443b65d4c85cf7ff2b5a7a683
Author: Ethan Van Andel <evanandel@lbl.gov>
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 96d0aaffd6a91068268aef77058216b32036e4bb
Merge: 6891882 c53ec80
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 1 14:29:40 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6891882c32dd0a035d95dee77856f6f0864596ee
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jun 1 14:29:19 2012 -0700

    changes for battra and naphta.

Tools/F_mk/GMakeMPI.mak

commit f2bc68c8d95e7b9e1fcff135818ff2fbd6f05f87
Merge: 7bdc6c3 821232f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 13:04:34 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing

commit 7bdc6c310748ece7ee07a440c05f6508b0587d7c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jun 1 13:04:11 2012 -0700

    chmod a+x plotsinglevar.py

python_plotfile/plotsinglevar.py

commit c53ec80ea9dbe6f18fe86905336c4438313417ac
Merge: 0e208d9 e69c6bd
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu May 31 21:45:19 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0e208d92f46f54de78800e859b85f9d720878c91
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 f4560fa8705362124fbc13fe039545a5d66fb7b3
Author: Ethan Van Andel <evanandel@lbl.gov>
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 e69c6bdf0cde192daecdaf25e37264797dce1eba
Author: Ann Almgren <asalmgren@lbl.gov>
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 b29b9365eac27879c70420b8ac79cf0cbefa9b07
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 09:54:56 2012 -0700

    No longer need cvs scripts.

Tools/F_scripts/cvs2cl.pl

commit 540b6f1819015d01e5a1152e5d0afccbd12c77c7
Author: Ann Almgren <asalmgren@lbl.gov>
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 66d612c53bd8ccb4704e47d4475ce9a832d61c23
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 31 09:53:13 2012 -0700

    Move Tools/C_util/regtests to Tools/RegressionTesting

Tools/C_util/regtests/Castro-tests.ini
Tools/C_util/regtests/Maestro-tests.ini
Tools/C_util/regtests/README
Tools/C_util/regtests/gen_compile_test.sh
Tools/C_util/regtests/radiation-tests.ini
Tools/C_util/regtests/test-Ubuntu.py
Tools/C_util/regtests/test.py
Tools/C_util/regtests/testnew.py
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 25643bf9f0271277328e42c84d28d844a37bcebc
Merge: 0a87538 1232211
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 10:46:54 2012 -0700

    Merge branch 'subcycling'

commit 1232211ff46ec47bd9270058b0db71fadd08c860
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 10:43:52 2012 -0700

    Minor fix to Where

Src/C_AMRLib/Particles.cpp

commit cc0d084a07aeecaf9a8938ffb387d825c24355ec
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Tue May 29 09:55:15 2012 -0700

    Removed redundant method declarations, changed to default param.

Src/C_AMRLib/Particles.H

commit 0a875389aef2915532ee8f59f6b12196df9efde0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu May 24 13:02:16 2012 -0700

    Changes for Aleks.

Tools/F_mk/GMakeMPI.mak

commit afa02079e7ffb62e2a9ea81864066594c6ee94a0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed May 23 21:16:36 2012 -0700

    builds correctly now after Ethan's re-org to add C_AdvancedTopics

Docs/GNUmakefile

commit af4058867f8242ef0ae3c51288a5bc594b703ed9
Author: Ethan Van Andel <evanandel@lbl.gov>
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 712baa3b2ed3d1c12f8ead06ca671df820c64d8a
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Wed May 23 15:05:00 2012 -0700

    Important bugfix to 2d hoextraptocc (seldom used)

Src/C_AMRLib/FILCC_2D.F

commit bd14f4cfd42be340a22e69ec0a0bd1f12c47d9f5
Author: Ethan Van Andel <evanandel@lbl.gov>
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 e20daad2d5638784d2d5d2c0d5cdc9c5eb1df2b9
Merge: cd6749f ceb063c
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 22 13:20:35 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cd6749fe0554fd1ea7e80c3d42837d445684aaca
Author: vince <vebeckner@lbl.gov>
Date:   Tue May 22 13:19:20 2012 -0700

    changed default PLOTPER test.

Src/C_AMRLib/Amr.cpp

commit ceb063cdc0c3a5d83aa3473e32c379770f47b109
Merge: 56054f7 bbf2ab3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue May 22 11:08:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 56054f7e6047dd094e1e57465b02102379be6cc8
Author: Ann Almgren <asalmgren@lbl.gov>
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 bbf2ab39298902895eda07dce395fc12dbb088d9
Merge: 6d2ed2f 451dea8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 22 10:25:14 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6d2ed2fa05c32d88afca7a415bdcc46ee511d9c8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue May 22 10:25:02 2012 -0700

    fixed a comment

Tutorials/HeatEquation_EX5_F/advance.f90

commit 451dea88f654c33ab3a6317c975e7726b65d4240
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 17ee12a0deb996d8ce758b8be0990342ec53cc06
Author: Ethan Van Andel <evanandel@lbl.gov>
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 c62e4cc066894184a2bc29b12e4d55c60adc0477
Author: Marc Day <MSDay@lbl.gov>
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 8754726883a876f01533c6871a7917ca86349edd
Merge: fdc92bf 2d04bb0
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Mon May 21 12:03:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2d04bb064d89cbd4a2c8800090b6c876b94b3565
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Mon May 21 11:27:56 2012 -0400

    remove explicit inf section

Tools/F_mk/GMakeMPI.mak

commit d0d9d98c6e6dbcbc578ed0ddf1ed8b5947f4aa9f
Merge: 6a6787b bca983a
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Mon May 21 11:20:27 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bca983a6967258d049154562bd441959039bd776
Author: Michael Zingale <zingale@xrb.astro.sunysb.edu>
Date:   Mon May 21 11:19:08 2012 -0400

    remove xrb specific section

Tools/F_mk/GMakeMPI.mak

commit 6a6787bd133f00101dc428d6823881910b40c3b6
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
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 c84606868b8876a6a0cec893267160c12901da7b
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:56:37 2012 -0400

    MAESTRO -> BOXLIB :)

Tools/F_mk/GMakeMPI.mak

commit c51e7c9585d797f0fcccd73fc47a9bcb37e153cc
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 36c3f731d2213e470c85dc75c21b938f2d251730
Merge: 3d09419 0610b80
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:33:25 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 3d09419378ee98f760bd7e7d4fe0e358b26bafd5
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon May 21 10:33:04 2012 -0400

    some pretty printing stuff

Tools/F_mk/GMakedefs.mak

commit fdc92bfc269693fa6b1d00d8c90eb6c42238ef5f
Author: Ethan Van Andel <evanandel@lbl.gov>
Date:   Fri May 18 14:31:02 2012 -0700

    More doc additions.

Docs/C_AdvancedTopics/C_AdvancedTopics.tex

commit 0ab9ff2fd3b38dcfd053e05508bc9f4a09d5852a
Merge: 48820a9 0610b80
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 15:38:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0610b80a99ce863b3d6a08c86339b8e853adabe2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu May 17 13:47:58 2012 -0700

    linear solver note

Docs/AdvancedTopics/AdvancedTopics.tex

commit 48820a9c61c2ad9456090d62a62ec0f48575f77f
Merge: 71e44f3 9962deb
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:46:26 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 71e44f371cab7cb76e6f82763989fd1e9ae458c3
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:45:57 2012 -0700

    Added Assertions to check vcomp validity.

Src/C_AMRLib/Particles.H

commit e074473779ee4a798160e3297351b156d3678bac
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Thu May 17 13:42:51 2012 -0700

    Added empty Users Guide section for "State Data"

Docs/C_AdvancedTopics/C_AdvancedTopics.tex

commit fc7a53e31f9b58dc4507576b1f3bbdd42c111251
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
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 bbc5ce94ae537cb45390d04dc773a1c652ef698b
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
Date:   Wed May 16 16:13:29 2012 -0700

    Added a UsersGuide Stub chapter for Advanced Topics with C++
    that will cover particles.

Docs/AdvancedTopics/AdvancedTopics.tex
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
Docs/AdvancedTopics/hopper_omp.run
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 1d695f9b508e5c454a1c057c6ceba5abc3599b51
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
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 704e65b2d732ef2793df216a8c242c30ae6c76ee
Author: Ethan Van Andel <evanan@kumonga.lbl.gov>
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 9962debb1b6e26544bf613f05e226f1539bf7e29
Author: Marc Day <MSDay@lbl.gov>
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 5e1524b60a6c8492f2217784dc3dde988d3da5ba
Author: lijewski <mjlijewski@lbl.gov>
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 ba72d50c4dd242b0816868a741129dd9e1cb6718
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat May 12 17:23:15 2012 -0700

    A first cut at InitFromBinaryFile().

Src/C_AMRLib/Particles.H

commit 2aa25131d9618841c4b432f8940caba50bed9305
Merge: 453bea1 2a5bc74
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu May 10 13:30:26 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 453bea1bab9017408aa35af35929145fd2728bc4
Author: Ann Almgren <asalmgren@lbl.gov>
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 2a5bc74bc21fe22b835869a92fd07bc449c01498
Merge: fc57013 32cd0c4
Author: Mike Lijewski <mjlijewski@lbl.gov>
Date:   Thu May 10 12:40:39 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fc57013247f74e82546b58500819d65f60f15262
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 63f67108894d0812d35653f671d7329b7e1a1e83
Author: Mike Lijewski <mjlijewski@lbl.gov>
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 32cd0c49001aaf03668e3d1a5d212cc5bf4099cd
Author: Marc Day <MSDay@lbl.gov>
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 9038476a978fe706453167821403a0a155e9e6ac
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:14:35 2012 -0700

    Remove since it requires that I remember to manually update it

BoxLib_Version.txt

commit f11cd49bb9dfc08d1da99ffc652373d40b0c01dc
Merge: 6644b70 4cab11e
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed May 9 19:10:54 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 6644b702ff7d7ecb22dadd3aedeb066dadfc260e
Author: Marc Day <MSDay@lbl.gov>
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 4cab11e34e1ad6890263ca239cf77cf07e0a5197
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 8 13:13:11 2012 -0700

    Merged in protected_divide() to AssignDensity().

Src/C_AMRLib/Particles.H

commit a93857b7c9df3c1887bb8ac2ded473739b433b48
Author: lijewski <mjlijewski@lbl.gov>
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 1882f77e408d5ea224a41d69f816049d4c92ad63
Author: Ann Almgren <asalmgren@lbl.gov>
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 47dd2fad9f3e7739f01445f4ede1576829dc318b
Author: lijewski <mjlijewski@lbl.gov>
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 35b713aa0cfe1643ace4264711608369f29500e4
Author: Ann Almgren <asalmgren@lbl.gov>
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 186e6f39ddb40d93eddfdf88770099dac2126062
Author: lijewski <mjlijewski@lbl.gov>
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 8c930a6ddde8e4512d80408d5e4ed84d94b6094f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon May 7 10:31:08 2012 -0700

    Some more BL_ASSERT()s.

Src/C_AMRLib/Particles.H

commit c02d3fc3d8b03806711643d1fa525c10dac009f1
Author: lijewski <mjlijewski@lbl.gov>
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 20c6420992edd5c0b61930fbb38859b4b48b15c9
Author: Ann Almgren <asalmgren@lbl.gov>
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 a768e14a63d404521edd820efa38cbeca7d5b545
Merge: aa2dff1 5fe1b8e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 17:42:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit aa2dff1f739dfa1e75dc571550214b9743caac52
Author: Ann Almgren <asalmgren@lbl.gov>
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 5fe1b8e5217068ca0f53aa076288f7ebf140d25a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 4 17:20:09 2012 -0700

    manual update of version textfile

BoxLib_Version.txt

commit 6ba1a4cc62fdd54e971eb8ffbcbe433b3d2ee623
Merge: 80f587a 83540a4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri May 4 16:50:11 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 80f587ae52631d08ece6f9386124b0321a13a60c
Author: Ann Almgren <asalmgren@lbl.gov>
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 83540a42df2d5d76da897171ea22fe93f3fcc57b
Author: lijewski <mjlijewski@lbl.gov>
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 66220caaccab3eb8a23139576745ee9904b03869
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri May 4 13:26:57 2012 -0700

    addition solved case

Src/LinearSolvers/F_MG/ml_cc.f90

commit 4e0be3cdfec38d52399e6cdae974333c2679cff7
Author: lijewski <mjlijewski@lbl.gov>
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 9aa3afdf7d76ffa8101505fb8a69d98ccb5eef26
Author: ajnonaka <AJNonaka@lbl.gov>
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 f452b228fa3944d2f3930ecdf69600d895820e9d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu May 3 13:10:29 2012 -0700

    fix variable name

Tutorials/HeatEquation_EX1_C/writePlotFile.cpp

commit 47f4c9087a28c9607f05d7d47febd5f2a5b0ba35
Merge: 67b3bda 2122156
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu May 3 12:32:55 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 67b3bda30e5b3c786cd1c75a9fce8993c92dc117
Author: Marc Day <MSDay@lbl.gov>
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 2122156551e54e2d543fa554847fc69dc6f14e5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu May 3 10:12:51 2012 -0700

    Add Sanchez-Pomraning boundary for radiation

Src/C_BoundaryLib/LO_BCTYPES.H

commit 821232fedb00cffb4c345a9ce9756816e186cc69
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 176f8d3ac60a8279bccace11b5469b5f1e00001c
Author: lijewski <mjlijewski@lbl.gov>
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 0a27fa70326b56f298e50db8dd7afb83a630532b
Author: lijewski <mjlijewski@lbl.gov>
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 6b2eafc09a5317451f449f2a68f97a8a4ec2c84b
Author: lijewski <mjlijewski@lbl.gov>
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 f003cfed49e455985bb2d5fd12f59dcb50146a6e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue May 1 11:19:22 2012 -0700

    A little cleanup.

Src/C_BaseLib/FabArray.cpp

commit 1c21cca08cc15f0f56a92f5b8d650ebee1c65cfa
Author: lijewski <mjlijewski@lbl.gov>
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 5efc3ca5c264ca9804a5a8b137f14353f78176c1
Author: lijewski <mjlijewski@lbl.gov>
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 8fdf0a141c5c6f7488560f1ca756717df79a7d46
Merge: 624695a 0a27a8d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 17:07:12 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 624695ac1feac5040453d3e80b3c8daac73ed0bf
Author: lijewski <mjlijewski@lbl.gov>
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 a341435c02b9af54324f0121b7da8fdb31df3a0a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 17:06:21 2012 -0700

    New sumassoc stuff appears to be working.

Src/F_BaseLib/layout.f90

commit 0a27a8d894960fb5d6def6191247be7f9f777a06
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Apr 30 16:32:45 2012 -0700

    Dang, wrong text, wrong place....might be better now.

Tools/CMake/CCSEOptions.cmake

commit b06cd6f94fcfa50476b8035ce51076ee4b625125
Author: lijewski <mjlijewski@lbl.gov>
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 dfab0704ca7ce021cce547bb4c1d9de1629d3515
Merge: 3b51563 ef541e1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 30 13:23:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ef541e1a2f7bda8c844c5cad8b0a90b1cfd3e4ac
Author: Marc Day <MSDay@lbl.gov>
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 3b5156323ce61171c4b98ef443a313cb47481a8c
Author: lijewski <mjlijewski@lbl.gov>
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 1d204bcccc27142e3bb62470290ebfb436551419
Author: lijewski <mjlijewski@lbl.gov>
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 8e6157e60622a3520bc69a3742a71df5d9854530
Author: lijewski <mjlijewski@lbl.gov>
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 485a3d1523ebdf8971a097aeec5b9ef7d2804ff3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 27 16:18:34 2012 -0700

    cover fig

Docs/Introduction/varden1.eps
Docs/Introduction/varden2.eps
Docs/Introduction/varden3.eps
Docs/Introduction/varden4.eps
Docs/UsersGuide.tex

commit 62d2ef15e313930020717abd3b85c086c136ee84
Author: lijewski <mjlijewski@lbl.gov>
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 0ad8a344384db228e7337393c6f7db4060f6a677
Author: lijewski <mjlijewski@lbl.gov>
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 d198246d383eb0799caf672035911706d01960df
Merge: 9722377 b7ee879
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Apr 27 09:53:40 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit b7ee8797a846862d6df53ccd90656fe538051ab5
Merge: eec86a8 8d30c31
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 17:11:50 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit eec86a8a2ffd0d7c5cd316daacfc919d7ef3639e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 16:59:24 2012 -0700

    some User's Guide updates

Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 8d30c31a790b8c35f81b6e8e5030fca1809538ef
Merge: 4ed1544 71333cf
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 15:53:09 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4ed154495c92fe66205badbcb7721ebdab590dbe
Author: lijewski <mjlijewski@lbl.gov>
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 8b1dd172ff2ec3fe1c49c2232455edb560813628
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 26 14:18:33 2012 -0700

    Some cleanup.

Src/C_AMRLib/Particles.H

commit 894daaf35e5b972a77c13cd688141914068ebc99
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 14:15:21 2012 -0700

    comments

Tutorials/HeatEquation_EX5_F/advance.f90

commit 71333cf94f615bed396e0d064cb80508aeb25f23
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 26 13:40:35 2012 -0700

    remove print statement

Src/F_BaseLib/cluster_f.f90

commit df2834a50c306b81f571dd63e43c737fbb8ce7b6
Author: lijewski <mjlijewski@lbl.gov>
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 8d7a7dc31fe01003a8d26838ca08d448fc793d3e
Author: lijewski <mjlijewski@lbl.gov>
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 87b5d03d22be81360ce912e56e0344bf29295856
Author: lijewski <mjlijewski@lbl.gov>
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 071ca932333b3bbdac89aaf3cbe31843dc10838c
Author: ajnonaka <AJNonaka@lbl.gov>
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 1c7a76fef6cababcf298877446c53a34a2538b89
Merge: 659726f e40ac7c
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 15:44:06 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 659726fabcebc6c13fef4ac91f3a2c5a25ac23ac
Author: ajnonaka <AJNonaka@lbl.gov>
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 e40ac7cf73288527207bab383e24f3a67343ef7e
Merge: 609601b e89b81f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:51:27 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 609601b0841425bc9c4c22acedf6d91c285cbd89
Author: lijewski <mjlijewski@lbl.gov>
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 e89b81f228b61c8dfa18dd73781fd7ad4ccac71e
Merge: a67a0b8 800d75a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 13:43:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 800d75a19e5798c8d257d1f790a65bbcffcfe46c
Merge: 282c629 9fc5bce
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:38:51 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 282c629c38ff041478f6e8ba4241281bc0bf4c9f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 25 13:38:38 2012 -0700

    Inlined some Box stuff.

Src/C_BaseLib/Box.H
Src/C_BaseLib/Box.cpp

commit 9fc5bce23e8323b352a51e47d728d88ca83cef22
Author: vince <vebeckner@lbl.gov>
Date:   Wed Apr 25 11:59:25 2012 -0700

    added comments clarifying creating a distmap with an array<int>.

Src/C_BaseLib/DistributionMapping.H
Tutorials/MultiFabTests/MultiFabReadWrite.cpp

commit 58122a511b60b71b0ca6c3ab4605bea693275174
Author: lijewski <mjlijewski@lbl.gov>
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 a67a0b83659f574a8257b08ca992e0ef0a90f583
Author: ajnonaka <AJNonaka@lbl.gov>
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 27dbe2ed6e9c7b6541db2183db1ac515c1bf49e8
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 10:54:46 2012 -0700

    update docs

Docs/AdvancedTopics/AdvancedTopics.tex

commit 5ec5da06aaf478268a60e7d736b8cb10d2cce0cb
Author: ajnonaka <AJNonaka@lbl.gov>
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 b3fb98e4619821f1109323f2a4e088191ac9f9a4
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 25 09:43:27 2012 -0700

    linear solver progres

Tutorials/HeatEquation_EX5_F/advance.f90

commit 9722377b8cb088f83865e85e8a6ed7d9b8859459
Author: Marc Day <MSDay@lbl.gov>
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 92cadbf7f85954ad0f1b5b2d12e53953e1180c55
Author: ajnonaka <AJNonaka@lbl.gov>
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 612a8782ebfbbcbdb8617fdfce0a096c27f23f8f
Author: Michael Zingale <zingale@jaguarpf-login5.ccs.ornl.gov>
Date:   Wed Apr 25 10:20:15 2012 -0400

    add compiler version

Tools/F_mk/comps/Linux_cray.mak

commit ae1e4cf398b432c66763c3742351f3c989a605fa
Merge: 0dcd55b 908c1a7
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Apr 25 10:13:09 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 0dcd55b72224cc12c235d13728288fd9eee1e708
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Apr 25 10:12:54 2012 -0400

    add support for compiler version # in output

Tools/F_scripts/make_build_info

commit ae5ed979ee6b83c9f4c8368323b9e8069a21bdd0
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 908c1a76f962d983546aae40df0ac9c45ec520bc
Merge: 6d8ebcf 168e559
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 16:58:58 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6d8ebcfccd602827264385da566262755fba7ce0
Author: ajnonaka <AJNonaka@lbl.gov>
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 168e559dc2d56b0de9fc601a312ef7ebff40fd2f
Merge: 3d9abca f73a8b2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 16:55:30 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f73a8b22b359dba93eed61478568e79452cd969d
Merge: 7370989 1a57bbe
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 24 16:08:52 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 73709895e3340d2b792951bc4ace0c35392d2f94
Author: vince <vebeckner@lbl.gov>
Date:   Tue Apr 24 16:08:29 2012 -0700

    fix for FlushGrids.

Src/Extern/amrdata/AmrData.cpp

commit 3d9abcad4bd878db7d00326754709b57045810ef
Author: lijewski <mjlijewski@lbl.gov>
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 86d960ec3c1bc8a0ff23d75f8ab5fee948052e9b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 15:01:27 2012 -0700

    Yet more cleanup.

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit 070f846fab343a9b2d8e133d26163bfced2e910f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Apr 24 14:41:50 2012 -0700

    remove local tag_boxes.f90

Tutorials/HeatEquation_EX4_F/tag_boxes.f90

commit c5e8949ec1bf7d98d5bb3e0c5814ac5a4858f7e1
Author: ajnonaka <AJNonaka@lbl.gov>
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 8730d64a147161f01e28f0fbb2529789f7b77336
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Apr 24 13:14:35 2012 -0700

    Some cleanup.

Src/C_AMRLib/Particles.H

commit 1a57bbe229149092fe9846821ccf0221ddcbbcdc
Author: lijewski <mjlijewski@lbl.gov>
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 6c731388968b5ed31dd08129fab5e3dea94c99c2
Author: lijewski <mjlijewski@lbl.gov>
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 f79f4663665cf2dca43b33affeaa4112c67a08f8
Author: lijewski <mjlijewski@lbl.gov>
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 751c5bba94709117e4c8455bd6311056e8c8f38f
Author: lijewski <mjlijewski@lbl.gov>
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 7eea992ed0ca2d8a5d9223976afca0c0f6d22836
Author: lijewski <mjlijewski@lbl.gov>
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 444b39bad3d62de1451389ae5e0f93d51f71b9d0
Author: lijewski <mjlijewski@lbl.gov>
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 1939a427607705e0760c73bd3d433b948b12e61b
Merge: efcf06c c985bde
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 23 08:51:32 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c985bde7118efd720f3cf27d68796d967c608e4f
Author: lijewski <mjlijewski@lbl.gov>
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 efcf06c4eaca00b1509cda4c9c6c86adea444961
Author: lijewski <mjlijewski@lbl.gov>
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 5c650255cc43b8c723aeb10da772a72d2a48cbfc
Merge: bcd119b 23cef65
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sun Apr 22 16:45:08 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bcd119b469cbd912a21841a2f9147df6d7ddcefe
Author: lijewski <mjlijewski@lbl.gov>
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 23cef65968bd4afc076872eabdf3ab997a0082f6
Author: ajnonaka <AJNonaka@lbl.gov>
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 c0e71b33dcf7d002f9d9e57f6811bd454156878f
Author: ajnonaka <AJNonaka@lbl.gov>
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 8fdb58b4eeaa492cd3e41246e0c982f1622e93ff
Author: lijewski <mjlijewski@lbl.gov>
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 bbf5f6147b04e37b6b912cbaca9f9ea6071c1f31
Author: ajnonaka <AJNonaka@lbl.gov>
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 eb3435be43c96c938b645586aa7411eea5ad2151
Author: ajnonaka <AJNonaka@lbl.gov>
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 7182a5288e966cb1bbc34b0d70527f732f1d55a0
Author: ajnonaka <AJNonaka@lbl.gov>
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 0926f26fbc5c50babf73fe97b1aad8a9db1dbeab
Merge: beabd79 95a0342
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 20:51:31 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit beabd798ada15803bf675e28686b34d3f7a6c940
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 20:51:02 2012 -0700

    note about new example

Docs/AdvancedTopics/AdvancedTopics.tex

commit 95a0342339ae5bb687e8bf75ce4bc5cfb5f105af
Author: Ann Almgren <asalmgren@lbl.gov>
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 f426bdfea6e3a0a6623a2ac9e9367ea7d58167a4
Merge: 0f4b6ac d21efc2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 13:29:23 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0f4b6acc7e726437c370f91eda475519ceb29bc2
Author: lijewski <mjlijewski@lbl.gov>
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 d21efc20dfed9bdf0d742911347b012c6df76250
Author: ajnonaka <AJNonaka@lbl.gov>
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 ee67042946923d1ec4c919cf71b9910a38c0674f
Merge: 7b3610e 5b43709
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 19 12:37:45 2012 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7b3610e85c07d7ae63085ff817fc3eae6726cd3e
Author: ajnonaka <AJNonaka@lbl.gov>
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 c274eec8ebaab74e1f793d1959444d9e197e8d03
Author: ajnonaka <AJNonaka@lbl.gov>
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 5b43709c9883a13e452e9b347fd26a52c5f5e816
Merge: 94d370d b33276d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Apr 19 10:41:00 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 94d370d184958acc49a7c087d6e2f8976418f2d0
Author: lijewski <mjlijewski@lbl.gov>
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 b33276d8799fb8214e38a8290aafdc53c4b934be
Author: ajnonaka <AJNonaka@lbl.gov>
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 e8c0619c08eb9bba0cbe582198442803ed664355
Author: ajnonaka <AJNonaka@lbl.gov>
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 5c56d01899aa6b6d60028ca2eec358ccbcf0e554
Author: ajnonaka <AJNonaka@lbl.gov>
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 8aed01d21a9cfac7fad3ff42d39ef2439e35146c
Merge: 9d7e33e 10a1429
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 18 15:29:43 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9d7e33ebe014715f4039aff1b12c871aaf8748d5
Author: Ann Almgren <asalmgren@lbl.gov>
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 10a1429b36c3284b55baa9703a10017cdea80229
Merge: 60edad2 6f77ef9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 15:17:54 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 60edad2ec9a19d09f77cc3f213d54fe5f50b3cef
Author: lijewski <mjlijewski@lbl.gov>
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 7dcc738ed300b0b6a34b7fea0a4e6930c085478d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 18 13:56:45 2012 -0700

    A little cleanup.

Src/C_AMRLib/Particles.cpp

commit f6e1cc92517bb5cb95a6b7dc7ba80dc0ec6db9a8
Author: lijewski <mjlijewski@lbl.gov>
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 6f77ef96015b4899b50b938e13b3999ebaa443cc
Author: ajnonaka <AJNonaka@lbl.gov>
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 d65120f92f0ed09775addf2d9b000f28058e1ce1
Author: ajnonaka <AJNonaka@lbl.gov>
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 30997f0eb204505bf05876b2412b4c650ea8618c
Author: ajnonaka <AJNonaka@lbl.gov>
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 0a2f540b2cb907df0047f97ff25538c3886dc43e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 09:17:57 2012 -0700

    tidying up

Tutorials/HeatEquation_EX3_F/main.f90

commit 380bff01cd8f3b6c944be363ec64456ef4959425
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 09:01:08 2012 -0700

    clean up tag_boxes, add comments

Src/F_BaseLib/tag_boxes.f90

commit 01f10e7fc73d6ad743f40459cf0e78ad26de55c0
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 08:51:25 2012 -0700

    comment

Src/F_BaseLib/tag_boxes.f90

commit fd19cb3dcbc3ca49640b0a415c81745f1ab92d80
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 18 07:10:39 2012 -0700

    comments in ml_layout.f90

Src/F_BaseLib/ml_layout.f90

commit 69796f5f67fac49506411ad7dd809960e95e4da5
Author: ajnonaka <AJNonaka@lbl.gov>
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 71b5dd80b20db01daba4e4d64c2759a5bf46e6dc
Author: lijewski <mjlijewski@lbl.gov>
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 b178158fff36c1c4a037ecce48109d7b2737ef50
Author: lijewski <mjlijewski@lbl.gov>
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 bffce84589a880bb4ab266893c870ec55670dfdc
Author: lijewski <mjlijewski@lbl.gov>
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 176aba0f52d033fb7ad8ff89416ca565136b41e7
Author: ajnonaka <AJNonaka@lbl.gov>
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 725a1daf3badce7077d6b029c825baba3edc90ac
Author: lijewski <mjlijewski@lbl.gov>
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 b31a9583435afc148a612ab45219092952b5e0da
Author: lijewski <mjlijewski@lbl.gov>
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 e4cdaf63cfb52a6b58fddd597c553ed507267eac
Author: lijewski <mjlijewski@lbl.gov>
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 ce00d5da92ae70a6e836b4b6b71d9e19c1ad5642
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 10:07:05 2012 -0700

    Didn't have my CrseFine fractions -> Fine correct.

Src/C_AMRLib/Particles.H

commit 24f4e711d42a8beff1b288d5574f7eb221bbdc18
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 13 09:16:08 2012 -0700

    Some more debugging tests.

Src/C_AMRLib/Particles.H

commit 7c7b1c10e2508bdb11f44bd0d9cf8579ee803920
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Apr 12 20:21:16 2012 -0400

    add support for 3 plotfiles

python_plotfile/contourcompare.py

commit 99ece003b29af6e1698650a7e4cc49871d0e29a0
Author: lijewski <mjlijewski@lbl.gov>
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 94dc612b3e81b96fa911428b162b3f0efcb2e9cb
Author: lijewski <mjlijewski@lbl.gov>
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 de1ec0fe4796a54b5b74d4553660f5c7f894fa59
Author: lijewski <mjlijewski@lbl.gov>
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 d6ccda35d362b65ce198b568d3723469fe9fe96d
Author: lijewski <mjlijewski@lbl.gov>
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 1cd4b38c13c121e75f9889ee3349cd97adbd7ee2
Author: lijewski <mjlijewski@lbl.gov>
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 497861ea6a411b13b3a39c2260747fd7a97c2189
Merge: 2cb87cd e769804
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Apr 9 17:33:56 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2cb87cd2f8a73918a0560aa08c0fc4256fbfec98
Author: lijewski <mjlijewski@lbl.gov>
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 e769804776586e55d5f68b044268584161ea1727
Author: ajnonaka <AJNonaka@lbl.gov>
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 3c7dbd9b388056d071e122ad8492fbec2d0598cc
Author: lijewski <mjlijewski@lbl.gov>
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 d65d66a713296b6bfb0956988c39a7ee3f658de7
Author: lijewski <mjlijewski@lbl.gov>
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 c451dcc982d850d69a0a3f64828d059b1f70baa2
Author: lijewski <mjlijewski@lbl.gov>
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 96326f32058323d89480e019fef8917707c40d8c
Author: lijewski <mjlijewski@lbl.gov>
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 e175c298b217a132ca5187ff9ebbb1144111234f
Author: lijewski <mjlijewski@lbl.gov>
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 ff25d19614406ede500a8a45d15150b67218d2a5
Author: lijewski <mjlijewski@lbl.gov>
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 46519366b98d4293225f22bcdea212ae0e0ed959
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 08:29:22 2012 -0700

    Final (hopefully) tweak to FineToCrse().

Src/C_AMRLib/Particles.cpp

commit 9c2aae8c8c997dd1e9ee48a49f41829b28fba0fc
Author: lijewski <mjlijewski@lbl.gov>
Date:   Sat Apr 7 08:26:55 2012 -0700

    Refined FineToAdd().

Src/C_AMRLib/Particles.cpp

commit 7c2ac0856d37ff74275cef72be4cf4ef87723f9b
Author: ajnonaka <AJNonaka@lbl.gov>
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 db12646d4dd3557083b4a451ab0552b6cda63605
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 16:55:29 2012 -0700

    tutorial

Docs/AdvancedTopics/AdvancedTopics.tex

commit 29d366224b644afadd8f3005d5bc9ad93ca10e94
Author: ajnonaka <AJNonaka@lbl.gov>
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 6a8cf291e2b60605f54741f5c24b275135351c43
Merge: 7cf62eb 7a5f4e2
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Apr 6 15:52:59 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7cf62ebba890ab615581a17eb5705f5a44050920
Author: lijewski <mjlijewski@lbl.gov>
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 7a5f4e21d096f9dd6d50c5c4f765d0350377fd4a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:50:29 2012 -0700

    forgot to add init_phi.f90

Tutorials/HeatEquation_EX3_F/init_phi.f90

commit e3b79c0453068e0dbbec6e5e4e59734d6c6df21f
Author: ajnonaka <AJNonaka@lbl.gov>
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 529ea6e4c4c59e56315894827c08e9266e85a5cb
Author: ajnonaka <AJNonaka@lbl.gov>
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 a37a564c0c50f590b289bad4cbcf903ab248597d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 15:00:13 2012 -0700

    destory the_bc_tower

Tutorials/HeatEquation_EX2_F/main.f90

commit 092ea38bd6bbef0ab3fede9dcecdc35b88ab1592
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 14:20:31 2012 -0700

    more Tutorial updates

Docs/AdvancedTopics/AdvancedTopics.tex

commit 1f037503a95febb773cc400bf8ed445c341f4495
Author: ajnonaka <AJNonaka@lbl.gov>
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 4235e69d631d19c6b7893ad5eb9ab7a824364fd9
Author: ajnonaka <AJNonaka@lbl.gov>
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 798d370dc28cc939cc6199296bac9b04cb8af952
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Apr 6 10:09:34 2012 -0700

    updated test problem description

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit 8f74abea6d5059eeaf7b52421ec303eb35c3a032
Author: ajnonaka <AJNonaka@lbl.gov>
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 52ed3255df36fc216cc01c8461801143cae39f38
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 22:22:44 2012 -0700

    bug in 2d bc's

Tutorials/HeatEquation_EX2_F/advance.f90

commit f2fbff443ea41a00c476e394fa04ba69605aa854
Author: ajnonaka <AJNonaka@lbl.gov>
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 0d9b6a177402df18b3c5056a49c452299d514ed2
Author: ajnonaka <AJNonaka@lbl.gov>
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 ae04300fe8ac87d0518477bdc8c6ab6b50ea8e67
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Apr 5 18:13:41 2012 -0700

    some documentation updates

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit a1d7e5ab52cc3eb36f346bc6b2d65b13d319d228
Author: ajnonaka <AJNonaka@lbl.gov>
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 7ca08631bd506414e824fa803feb30feb4ef7f8d
Author: ajnonaka <AJNonaka@lbl.gov>
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
Tutorials/HeatEquation_F/GNUmakefile
Tutorials/HeatEquation_F/GPackage.mak
Tutorials/HeatEquation_F/README
Tutorials/HeatEquation_F/advance.f90
Tutorials/HeatEquation_F/init_data.f90
Tutorials/HeatEquation_F/initialize.f90
Tutorials/HeatEquation_F/inputs_2d
Tutorials/HeatEquation_F/inputs_3d
Tutorials/HeatEquation_F/main.f90
Tutorials/HeatEquation_F/make_fluxes.f90
Tutorials/HeatEquation_F/write_plotfile.f90

commit 2a03e8425e77437250c8fe5fc2befb737c31fbfb
Author: ajnonaka <AJNonaka@lbl.gov>
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 15d3d3f53b454adedc98a53382cf2c3b761c3695
Author: ajnonaka <AJNonaka@lbl.gov>
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 33ba0848c5e7364697b6609bfb6c5a889c760b9e
Author: ajnonaka <AJNonaka@lbl.gov>
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 1f57c910a56a3c2b4208abe91d21d59ad88622a9
Author: ajnonaka <AJNonaka@lbl.gov>
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 6b75f233e221e2b1ca35e3c59e67958e6b4c2d0b
Author: ajnonaka <AJNonaka@lbl.gov>
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 13ffabbb0a5fb20fbf6bf7706145e9bb06ba3e99
Author: lijewski <mjlijewski@lbl.gov>
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 37676d98c1737a09613f5f6ed8251042911eb80d
Merge: 7a47cb2 742f313
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 5 13:45:22 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7a47cb261a67a1cf3a1e9d6ff6b427f40a985d09
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Apr 5 13:45:13 2012 -0700

    Fix call to layout_build_ba.

Src/LinearSolvers/F_MG/ml_solve.f90

commit 742f31372f32d1bf3cabd8941116524fdfdd5ee9
Author: ajnonaka <AJNonaka@lbl.gov>
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 127a64a3cc05d1030ecda6b8529ca692aa838c50
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 15:38:47 2012 -0700

    latest

Docs/AdvancedTopics/AdvancedTopics.tex

commit 8f91b26363aba509b1907dffd8deb422e67d105d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 15:38:23 2012 -0700

    forgot to commit this

Docs/AdvancedTopics/hopper_omp.run

commit 623c4fb80a087095ab6e22c18e3abc4bde091778
Author: ajnonaka <AJNonaka@lbl.gov>
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 fc001cacd70e4310111febb37a35dd9b561dfb48
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 13:28:08 2012 -0700

    code comments

Tutorials/HeatEquation_EX1_F/advance.f90

commit b4a06457c0e53d192ffa2b2cdd9687bc41df30ed
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 13:26:57 2012 -0700

    comments

Tutorials/HeatEquation_EX1_F/advance.f90
Tutorials/HeatEquation_EX1_F/main.f90

commit 83582dd591477f6eb406f505a284e56a21981668
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 12:47:24 2012 -0700

    more progress on User's Guide

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit 83cb73aa1ece771d366dd633f76d6a90b737e665
Author: ajnonaka <AJNonaka@lbl.gov>
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 7528cafa42546610d8f12bff21892e92943d58de
Author: ajnonaka <AJNonaka@lbl.gov>
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 e6c3b207456f91d924dbebfd3253f8d2f4706b9c
Merge: 6bf50c1 4434821
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:55:44 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6bf50c19e46998ae87b80ca7bc399ca9c081e611
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:55:19 2012 -0700

    rewriting advanced topics chapter

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/UsersGuide.tex

commit 93241b4c58e49e5888128239d36acfc719b01423
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Wed Apr 4 10:31:17 2012 -0700

    update to the new layout_build_ba interface

Tutorials/WaveEquation_F/main.f90

commit 4434821360ae62ff54ef539779121a44636a82e0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:28:39 2012 -0700

    Fix the call to layout_build_ba.

Tutorials/Exp_CNS_NoSpec/main.f90

commit 44e38f803aa4be0a5cf6a6d3d4e63744683d86b6
Merge: f8a6c08 42596e5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 10:26:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f8a6c0800885de0c2d65688ee6862c487109b970
Author: Ann Almgren <asalmgren@lbl.gov>
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 42596e528fc550d4759a8f9e4deebdc5cabddc07
Author: lijewski <mjlijewski@lbl.gov>
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 3645722c0054fbe8ce4bc248f1ff88a7514ec26b
Merge: f6b98b5 514040f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Apr 4 10:12:16 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 514040f9fa8b16a865b2f0eb9aee25bfe7326993
Author: Ann Almgren <asalmgren@lbl.gov>
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 f6b98b596613694409ba9badb05babf862959a32
Author: lijewski <mjlijewski@lbl.gov>
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 ff19364c0dcb1f65801988651e4763e9f6dda6e2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 09:15:48 2012 -0700

    Add 3d inputs file.

Tutorials/HeatEquation_F/inputs_3d

commit 1f6035cf10332880fb5dd6db9475d50a9e62a044
Author: Ann Almgren <asalmgren@lbl.gov>
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 47ae657a2ae4f5f730b2cd7ddb27d1a2faf456fc
Author: Ann Almgren <asalmgren@lbl.gov>
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 af079ee7bbb12d9b984e3716330166e191091452
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 08:01:15 2012 -0700

    Added README.

Tutorials/HeatEquation_F/README

commit 0196078ef89ba993ea631e269d4a691db22a85af
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 07:57:50 2012 -0700

    More cleanup...

Tutorials/HeatEquation_F/define_bc_tower.f90
Tutorials/HeatEquation_F/main.f90

commit 2f0e4082f36fe0bf37ff5543d49964a0d8e97708
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Apr 4 07:55:23 2012 -0700

    Add more comments.

Tutorials/HeatEquation_F/main.f90

commit a73975856df21b4f98849d7f97b454475266b531
Author: Ann Almgren <asalmgren@lbl.gov>
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 04a458206dfc0a389aa54a0024ba5e46ad33bc74
Author: Marc Day <MSDay@lbl.gov>
Date:   Tue Apr 3 12:41:31 2012 -0700

    What the heck...declare v1.0.0

BoxLib_Version.txt

commit 2fc4bd3a77807d0a5f054135d1000472ed2c0206
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 15:51:34 2012 -0700

    Changed := -> : in a couple places.

Tools/C_mk/Make.defs

commit 56ad6f9df48abb6a9ebcc888eddbc0e7c96cbda2
Author: Marc Day <MSDay@lbl.gov>
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 f333a72a1cd74813fb32cdd9eeff77eacca7f18e
Author: Marc Day <MSDay@lbl.gov>
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 39296ce3cb58c67df08a9722f4841cbfe0830c6b
Merge: 2675ff6 9f44ff9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 07:17:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2675ff663158711b8678f75c5a7be905de7df5aa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 29 07:16:48 2012 -0700

    Fix from Manuel Cotelo.

Src/C_BaseLib/FabArray.H

commit 9f44ff907c8a64f21342c979bdd5019c7946f548
Merge: 427e2ee 0452899
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 28 10:38:03 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 427e2ee6a2690c74b4d7a23badff954f77ca786d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Mar 28 10:37:43 2012 -0700

    added FillBoundary.

Tutorials/MultiFabTests/MultiFabReadWrite.cpp

commit 045289947b8e41a20e2c8e77a82f34926e1ad605
Merge: eed78a6 052eaa8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 28 10:33:21 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit eed78a66ca694f0a75cd27c88495203d6534b839
Author: lijewski <mjlijewski@lbl.gov>
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 052eaa8d82bd5de60128ab97fdd3b09781511d32
Author: vince <vebeckner@lbl.gov>
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 c14baf6d8e8af32b56537e5c61b8b5aea5acb04e
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Mar 22 12:35:26 2012 -0700

    mothra no longer overrides GNUmakefile to force Intel compilers

Tools/F_mk/GMakeMPI.mak

commit 1e075a4fa187b574a6139d9cc9688c2354f5957f
Author: Matthew Emmett <memmett@unc.edu>
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 880d095df1edb33a09efd1ac2446558f2ea32444
Author: Ann Almgren <asalmgren@lbl.gov>
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 b57df6d8ff1f497e2d34167c3254830ef66ca421
Author: Marc Day <MSDay@lbl.gov>
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 280ad87841a0387d3573b59f3acf2e22e355f5ee
Author: Marc Day <MSDay@lbl.gov>
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 37ecccc56b3d29139a40e6cd1cd0fdcbc0cf618a
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 115a3d43d02dd929c06792b416c8458d007cd650
Merge: f233bf4 3a5b8ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Mar 15 14:13:05 2012 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f233bf4e0552283cd62dd03e101370c004222142
Author: lijewski <mjlijewski@lbl.gov>
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 3a5b8aefd7c24779e7ee590499e3cdf2603ef5c1
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 13:19:32 2012 -0700

    Make particle replication stuff dimension independent

Src/C_AMRLib/Particles.H

commit e88ecbcce4822c3e4191734c1db2953008f0b530
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Mar 15 13:17:58 2012 -0700

    Add define for particles used in some app codes

Src/C_AMRLib/Make.package

commit 8240508509155564ffc71df421f2fbfee1339174
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 1f12c38fea8b0cb9bc6a11d53ba712c29df5ae62
Merge: 4bc5ddc c72eb87
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Mar 14 13:37:52 2012 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 4bc5ddc875a2ce35e7157b1858658902f761a168
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 5720d077ee00d957ec6446f7de85254ba797600d
Author: Ryan Orvedahl <orvedahl@bender.astro.sunysb.edu>
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 c72eb872410f2a5aa8a09ffeb125ee0312730fc0
Author: lijewski <mjlijewski@lbl.gov>
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 ed27f71a2e1cfd4af40e6e1278978032ec918702
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Mar 13 12:44:01 2012 -0700

    Removed -mp and added -ip for Intel.

Tools/C_mk/Make.defs

commit cd9b9fb1409a22e10c4416507df58fe41e5a3093
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Mar 13 12:43:34 2012 -0700

    Commented out some really old Intel Version 5 stuff.

Src/C_BaseLib/winstd.H

commit 0fb4b874dd676323407ec1fcfd7306875a2be829
Author: lijewski <mjlijewski@lbl.gov>
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 02c83979bf25da437b2fe388d0f921dd216597c9
Author: ajnonaka <AJNonaka@lbl.gov>
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 1f7d2590467a4245c237b8f323d495207fed090e
Author: lijewski <mjlijewski@lbl.gov>
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 17225b246343771e1362cd990333455df6077640
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Mar 7 12:55:33 2012 -0800

    Fixed to not need/use LinOp::bndryData(BndryData&).

Tests/LinearSolvers/C_CellMG/main.cpp

commit 6a4201eb29259a1b3025eade6912757a0fbb0828
Author: Matthew Emmett <memmett@unc.edu>
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 54eb2dacf3d1ce5fdbe2b059620f11e6e1c222d2
Author: Ann Almgren <asalmgren@lbl.gov>
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 c2ceeb4879d9b9e05f2ee29127c428ae5b5d843d
Author: Ann Almgren <asalmgren@lbl.gov>
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 7da46fc92dcb74f98a0220ab576acde5ced83cae
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Mar 1 14:22:07 2012 -0800

    Add REAME for the multigrid tutorial.

Tutorials/MultiGrid_C/README

commit 46ff83b4021704ecf58a2d2666cdbe1f44dc79fe
Merge: 0452a25 cc9236e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 29 16:38:30 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cc9236e49a9b2d9babaff2bd1cc4a42e6b14f82e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 29 12:58:24 2012 -0800

    Commented out a couple warning messages.

Src/C_BaseLib/FArrayBox.cpp

commit bc6eb37c9fb86845989dc03f381c1f12a833262a
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Wed Feb 29 11:17:16 2012 -0500

    get this compiling again

python_plotfile/GNUmakefile

commit 4f9614fc9fc649881ac7450b192748fde8afdcd8
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 ae66a9ab804723415aec22e3a7cd2d3c02a11c9a
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 5681ff56f8f569cd7598d0920792517f3718db0a
Author: Ann Almgren <asalmgren@lbl.gov>
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 51e5a3c1c1a94734fa89723cbc464d69dabbb1ea
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 15:07:11 2012 -0800

    BOXLIB_HOME default should be ../../.. not ../..

Tutorials/MultiGrid_C/GNUmakefile

commit 179448c17609121d570366aa28dbc7beee73683c
Author: lijewski <mjlijewski@lbl.gov>
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 f78e11d9b1a5de57e0f685d99d08c02e22ce6465
Author: lijewski <mjlijewski@lbl.gov>
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 5c940c11d5afba1508e340bdc749793b4e84e85f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Feb 23 13:45:58 2012 -0800

    Make copy constructor & assignment operator private.

Src/C_BoundaryLib/FabSet.H

commit 53de5fac7da00066329441f45e7c5d31bc786268
Author: lijewski <mjlijewski@lbl.gov>
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 d6cacd007daef8f26f5a9c751317471ee93bba2b
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 0452a25525b6ddf5722b591d9a31c5da19cf2089
Merge: 53d48d7 121ab03
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Feb 21 15:40:31 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 121ab03d54c2a7488f13203d5fb35b2205e95fd9
Author: John Bell <jbbell@lbl.gov>
Date:   Sat Feb 18 16:16:28 2012 -0800

    added note about how to build

Tutorials/Exp_CNS_NoSpec/README

commit 4a7942a0becf274f46e46f2f9277c1ef0af89896
Author: John Bell <jbbell@lbl.gov>
Date:   Sat Feb 18 16:14:25 2012 -0800

    added a README to the compact app

Tutorials/Exp_CNS_NoSpec/README

commit e07414343189ffed8e6ad422f11897afaf38da78
Author: Ann Almgren <asalmgren@lbl.gov>
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
python/timestamp_02
python_plotfile/GNUmakefile
python_plotfile/contourcompare.py
python_plotfile/fsnapshot.f90
python_plotfile/plotsinglevar.py
tutorial/GNUmakefile
tutorial/fspeciesmass2d.f90
tutorial/fwrite2d.f90

commit bc8926278143a1ab87560c17ace1cbcc02d5f073
Author: Ann Almgren <asalmgren@lbl.gov>
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 12aedbd36b7912164dde5b49278001e1490375b5
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 0c521c64f6e5e05ff91e877d72734cc071919ef4
Author: Marc Day <MSDay@lbl.gov>
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 d99d6888e4f4d9eafc3f61f211a6c26feac91235
Author: lijewski <mjlijewski@lbl.gov>
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 53d48d79131c4b0bc96c954c4941512128c607d7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 21e3faa66b64a3ec42fa7bbb690d1dabf02bc34c
Author: lijewski <mjlijewski@lbl.gov>
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 5ef0214fc64cd6d671480490c6e0839c56318f7f
Author: lijewski <mjlijewski@lbl.gov>
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 ad316cda87891b33af0144f25a5e7739b2b2805b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 15 10:37:46 2012 -0800

    Make calculation of courno in ctoprim() optional.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit efda4046347062a43653a3a125ce618d841200e6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6f195344494010d4a95b481d9e7fef823ee31fdd
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 15:53:05 2012 -0800

    Fixed typo.

Tutorials/Exp_CNS_NoSpec/write_plotfile.f90

commit b3dd826a12e437b68f052c78e516c6c2da3dac4b
Author: lijewski <mjlijewski@lbl.gov>
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 d9f12caf29f8b0b133cf4a3b948dc8f89b908983
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 15:35:59 2012 -0800

    Moved final output statement before boxlib_finalize().

Tutorials/Exp_CNS_NoSpec/main.f90

commit ae5a621f27287ff6d66374fe064e1edf67abe4b5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 14:26:42 2012 -0800

    Some code rearrangement.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit ac650ebac49d68674949df907b6148ca12cca719
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:44:12 2012 -0800

    New inputs file.

Tutorials/Exp_CNS_NoSpec/inputs.jbb

commit 704c64152a1de7ae562084f8a95b86c6c472a164
Author: lijewski <mjlijewski@lbl.gov>
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 154f3e1a91111c608812d5b7ecfde2ab8d278ad0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:26:18 2012 -0800

    Replaced some divides with multiplies.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 11f5bdcfefe5ff8c2acfe58d8237355fa0b9bcda
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 13:03:45 2012 -0800

    Some memory and performance improvements.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 51c07ce5ce2945a6e56f19e2695da3e332d63c75
Author: lijewski <mjlijewski@lbl.gov>
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 ee134688620c874e7896c230970f0d44b758c3b3
Merge: d840576 0b4702e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 11:12:14 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d84057616f447f2a41196ea68783ac817b866c1a
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 11:12:04 2012 -0800

    OMP init_data

Tutorials/Exp_CNS_NoSpec/init_data.f90

commit 0b4702e7491873e40d2d6defcf5f4aad7518594c
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 b7d54afbbdc3f4ca433f9b20c929509fe05ce478
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:48:54 2012 -0800

    Some OMP tweaking.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 71ec1b3d993ae7d89413d76323d146aa89f0f68d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:23:10 2012 -0800

    OMP'd diffterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 9c8e925b574dea8cc2d8b2729d12bd13b3528c17
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 14 10:01:44 2012 -0800

    OMP'd hypterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 08faa433272cba5b2213550ef0b9a5b552786d2c
Author: lijewski <mjlijewski@lbl.gov>
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 623b8940699a726d6da44871d41fa33b87434982
Author: lijewski <mjlijewski@lbl.gov>
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 d8b6c68402d378563cc08c023aa7c6c2ee7f85ee
Merge: 4877c55 f11d3be
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 20:28:22 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4877c5587d3daa7682072cf10740040ae2fcf908
Author: lijewski <mjlijewski@lbl.gov>
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 3cc1401c74bce16cbb60934e12a11d4cbfb95e99
Author: lijewski <mjlijewski@lbl.gov>
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 f11d3be3ac1ac18cc29acfbcbb8a8c5c59d72f78
Merge: 521d1fd 4e8ec03
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Feb 13 20:39:01 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 521d1fd6a271dddd547905863b3567e79a732cd1
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 4e8ec03af47dad0b878314b137cbafd2291c0681
Author: lijewski <mjlijewski@lbl.gov>
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 fdb385607352754ea0bd548dec4a2f69376a7757
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 16:29:09 2012 -0800

    Added a couple more named constants.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 1ddb104a7e9385766d8b3082627c811a42181ba3
Author: lijewski <mjlijewski@lbl.gov>
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 5a0b3003cb87bf9128d968f79652c01d65b5ef96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 15:48:12 2012 -0800

    Some work getting diffterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 9ad9192e9e0e264a8271cba0be2e02c8e4cca409
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Feb 13 15:20:48 2012 -0800

    Actually call ctoprim() & hypterm().

Tutorials/Exp_CNS_NoSpec/advance.f90

commit e7a3df79ab7f8d42db923bf6db256bb118f7aa3b
Author: lijewski <mjlijewski@lbl.gov>
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 6eeb24926850a2dc704c12789f7a05d575f173b6
Author: lijewski <mjlijewski@lbl.gov>
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 d6fbcf1834bd345af83339b24740907b1aa80c15
Author: Marc Day <MSDay@lbl.gov>
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 4c0a400aacdb34c30d6fcdb391aca35639dae19f
Merge: 1e03915 c7830e6
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Feb 10 20:44:45 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c7830e6c77a33ad6187e159d9f2ef770aecea032
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Feb 10 16:02:04 2012 -0800

    Some cleanup.

Tutorials/Exp_CNS_NoSpec/advance.f90

commit 6357e1abb9ff8153ccda2909ee544608ecfb8cca
Author: lijewski <mjlijewski@lbl.gov>
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 5d55ea7fc30c18f79831e64c76c8a24188884161
Author: lijewski <mjlijewski@lbl.gov>
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 c8d26c262ad2d249f971120f1d46a25ca890801d
Author: lijewski <mjlijewski@lbl.gov>
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 5d5ef8d6e1e73ae94a91f57f722eeefa3224769d
Author: lijewski <mjlijewski@lbl.gov>
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 bbd95909a171e491648b8884824e2ec5f125cdd2
Author: lijewski <mjlijewski@lbl.gov>
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 74d3da57ac3a0633c05bbe183c63a504e2056586
Author: lijewski <mjlijewski@lbl.gov>
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 4695e77d9f41b6f445408315c0fa4c4475ecee6a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Feb 10 08:26:27 2012 -0800

    Put Mike's fixes in for gcc/g++.

Tools/C_mk/Make.defs

commit 42db55787ce633e95fcd3bb952eaa0abcb4bae9b
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Thu Feb 9 16:31:03 2012 -0500

    add a sort to the test problem

Tools/C_util/regtests/testnew.py

commit d13bf9506a878f001a41c5e25a2361e01aef7eea
Author: Ann Almgren <asalmgren@lbl.gov>
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 054ac4696b0e1e08435723314bf408e5f16c1856
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Wed Feb 8 20:02:30 2012 -0500

    fix some typos

Tools/F_scripts/write_probin.py

commit f95cbd6017915fa9901126a25bc3b0f50835daa3
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 3c3fefcd7fa4382fc5d5689616e1d3dfbdae0ce0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Feb 8 09:14:26 2012 -0800

    A little more generalization in support of Aleks.

Tools/C_mk/Make.defs

commit 2b9da5fe2278c31728555b1e83cad5f3d1c7088c
Merge: 9844778 ab77517
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Feb 7 19:33:55 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9844778feafdc84e624077f646b8544052809bfa
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 ab77517406cf3223ee7c5b87d30ee2fe5ca68a0b
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 d83c6c416c329134b219a3e77f88c945b8bf2a59
Author: lijewski <mjlijewski@lbl.gov>
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 d30ef9f15cbe320921f9a37503f07fcee5918021
Author: lijewski <mjlijewski@lbl.gov>
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 8b6c07c7e4b4cd8c068116f16a7d20330edf181f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Feb 7 10:05:24 2012 -0800

    BOXLIB_HOME macro wasn't quite right.

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 7ed675942b5d05bb6430e3fcbabd0ffbe88114c2
Merge: cf4caab 0ba36a8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Feb 6 14:10:14 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cf4caaba7e07233dddd91577bb20dc6faf290d15
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ba36a85a76eec3951ca3c8a22abbcdbeef138e2
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 a415f6cecc4fdd0ec6e478805f27127861a13038
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 1d98cb2eb1f28356fa5dbfd6f2f3f5bae3dfa336
Author: Ann Almgren <asalmgren@lbl.gov>
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 f6cc9ed18fe1f1337b32537b124d10ecf0d03bf5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cea650320323a69818dffe5f316a33eaf791f0a7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 686cd540f2f91c3b60bc72f6ff5f4f165fb1f9cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 877210180c8b8a413ce36f45034ed0898f21373d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Feb 1 17:00:03 2012 -0800

    put subtract_divu_from_rh back

Src/LinearSolvers/F_MG/nodal_divu.f90

commit ca02edb9d8a6fa2d38f5cbf1be77bca4c7daad0f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a2d6cdca3d04fe8702d9dac4f7e20636976d82ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cd5e5ef1b5c42edadace7394a72485050dc26a6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4a943b9c62ccc99befff52e903546d8aaab3e5f5
Merge: 306e286 aa2f7db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 31 17:27:36 2012 -0800

    Merge branch 'dev'

commit aa2f7db79e32ef57218b86014dbc6af639481e08
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 306e286be05863043669bf4e810d5aa7796290ff
Merge: e836c31 19de476
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Tue Jan 31 19:01:04 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e836c3128c6822752147d82d552c4871a4c94890
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 19de476e6c36f24c7799ad3b84f6f15b7a08b50d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6575dc69a145763ca183a5dd8a4bd93a5c951757
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 abb3405d8bf9bd46bdda1755238f0a48a1b32472
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0b26aaf395646e7c6e04f5ea9187b243260577bd
Merge: c7881bb 6173aa3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 27 13:15:47 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6173aa36b71032c29040502b9493a36c4c5eb678
Merge: b785eb0 ea544ba
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 27 13:12:27 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit b785eb0b7e495fb729b94f91b0a0017bfc93c80c
Author: vince <vebeckner@lbl.gov>
Date:   Fri Jan 27 13:12:09 2012 -0800

    set version string for fabs and multifabs.

Src/Extern/amrdata/AmrData.cpp

commit c7881bbb2f9fefe017129c65e5ff3dfc8dbfa4d4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ea544ba8fe1db22c657fe0a83ee1365c4e0481da
Author: lijewski <mjlijewski@lbl.gov>
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 2a6d196f6952210b0bf8a0d7d825c51ebd4f4557
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:49:50 2012 -0800

    Add some comments

Src/LinearSolvers/F_MG/nodal_divu.f90

commit fe231bdc5bcb32704314c7542557eaa080dde525
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 26 13:43:26 2012 -0800

    clean up

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 4445d01ec5b196f38c71dbd978fe0f90a8603cb4
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1e03915a1827a80de7b811cf2a75c9d40140c4c9
Merge: 2cdd6ea 94f30ab
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 25 16:38:01 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2cdd6eaa16266f5e90f39dd18d469ce51775f46a
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Jan 25 16:35:24 2012 -0800

    Remove CMake hack suggested by one of the Amanzi folks

CMakeLists.txt

commit 94f30abbfb6674169a7ea366a101f2f81b78235f
Merge: 30bd8eb bf3bb54
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 20 13:24:31 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 30bd8eb9336009461a9e6c58efbfa87f411ca1f3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 20 13:23:38 2012 -0800

    Fix a parallel bug

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit bf3bb541d409227d5959d26fa6eaa56df1891099
Merge: e2c5b3a d9344e6
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Fri Jan 20 12:08:12 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e2c5b3a7935d10874e7eeac83ed243e5869767d0
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 d9344e6f5d8a5fa1e8c781a68714e32fe9381da6
Merge: 14eafc8 9a5bb1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 19 17:17:14 2012 -0800

    Merge branch 'dev'

commit 9a5bb1dd0c42d2877b6d77b3047f1ce74ea4a80b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 19 17:10:50 2012 -0800

    3D implemented for nodal sync residue.

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 14eafc8eab3b6b6262f44d867a5889c7dcf4dad0
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 17:00:14 2012 -0800

    rle update pubtest 4

Tests/IOBenchmark/README

commit c75b87ac1bb85d3dbbfa198cc57d01bcecda9e3f
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:46:28 2012 -0800

    rle update pubtest 3

Tests/IOBenchmark/README

commit 4a253b7365e0c1a0ed947847a8c99185c85bd2ff
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:43:18 2012 -0800

    rle update pubtest 2

Tests/IOBenchmark/README

commit 98235ea264bb643ab08a99a50a788c6b9055df90
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 19 16:38:05 2012 -0800

    rle update pubtest

Tests/IOBenchmark/README

commit ae9be45fc966bb7cecd45da405765240de4cc81d
Merge: 2324849 e383f0b
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 15:49:48 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2324849545f7f83bffa0a81b0011db04da609b74
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 15:49:28 2012 -0800

    rme update 3

Tests/IOBenchmark/README

commit e383f0b7cf0dbfb337f387eabcfe96df5d5b3457
Merge: cef5902 2362078
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 15:34:42 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit cef5902a468455af7f566c8076e21b55782c7dc9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 18 15:33:55 2012 -0800

    Fix a few memory leaks.

Src/LinearSolvers/F_MG/nodal_mg_cpp.f90

commit 23620784baeffe76099f7af97354b577f4b25029
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 11:19:14 2012 -0800

    rme update 2

Tests/IOBenchmark/README

commit 620d0dad51d7418cf6be0b9ebc214b984520cc1d
Author: vince <vebeckner@lbl.gov>
Date:   Wed Jan 18 11:08:17 2012 -0800

    rme update

Tests/IOBenchmark/README

commit 82ef714d345a8208027d6efeb4431127421f69a6
Author: Michael Zingale <zingale@inf.astro.sunysb.edu>
Date:   Tue Jan 17 15:56:48 2012 -0500

    update inf for new F16 install

Tools/F_mk/GMakeMPI.mak

commit e647a6dc9fd1c636b0a5968395d47170d4ae49fc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5db1e9f479858555c972c4355af23327bbf2da7a
Merge: 521c2aa b843d64
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 14:26:40 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 521c2aa49cb5cf8bcb2a8e452592ef8a4040abbd
Merge: 2efda7d 37fb657
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Jan 13 14:26:23 2012 -0800

    Merge branch 'dev'

commit 37fb657834a1ca6c157ab899434d7618295e7876
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b843d64ab6f6dd75c23dcb90316cda81e40d30ec
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Jan 13 08:25:43 2012 -0800

    Some cleanup.

Tools/C_mk/Make.defs

commit 9f78fc730467518a7b5c14818d8461b9f58c88c7
Merge: 7676f02 57ac1a1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 21:03:39 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 57ac1a1967fc3590b03f1dd0a248f93e28733972
Merge: bdbacfe 0564f8f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Jan 12 20:27:37 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7676f02bb3e348bbeaa03a9b4a439c9bab118bdb
Author: lijewski <mjlijewski@lbl.gov>
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 0564f8fbd996aea0c4cf9a57096d763c2ae8da43
Merge: d49e265 2efda7d
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:18:45 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit d49e265e05f1e2fbb40ebaa9bad2cfdd2733c2da
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:18:29 2012 -0800

    more 2D

Tutorials/MultiGrid_C/COEF_F.H
Tutorials/MultiGrid_C/main.cpp

commit b191d1bcacaade9f151d9ee257b94b86726d639b
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Jan 12 17:17:18 2012 -0800

    switch mpi on hedorah

Tools/C_mk/Make.mpi

commit 9b4eb6e605a2351ce62e78d29f0a2ac19a9ef488
Author: Marc Day <MSDay@lbl.gov>
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 bdbacfe342bb2ce4117c6b990f0e0db27700ace7
Author: lijewski <mjlijewski@lbl.gov>
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 2efda7d6569005aa3d03b254e1292dcfe7f778d6
Merge: d7d4c02 66213b9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 16:58:12 2012 -0800

    Merge branch 'dev'

commit 66213b92da3767b1a5ae2dd82a7eafa044d9de8d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d7d4c021be3c0c77ca1577a5a0a1244fe303b08f
Merge: 8fde59b 8435b76
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 15:35:28 2012 -0800

    Merge branch 'dev'

commit 8435b76cfc242940071770cf14e2af2adf8a234e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8fde59bdd029b689b93990149258ed69bd1c8581
Merge: 201c5ad 64314f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Jan 11 11:00:41 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 201c5ad000003229842628c4f982493b3d3364bd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 64314f2d96518256173d5f1dacc9d35c3c7695c3
Author: ajnonaka <AJNonaka@lbl.gov>
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 7510803ad377fff3656e5f1cfc1905b73389deea
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 17:40:37 2012 -0800

    starting a daunting documentation

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex

commit d374d653fc70b30ae29c3d0ad4f3b7065bb716e7
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 16:35:45 2012 -0800

    moving this

Docs/GettingStarted/hopper.run

commit a237ef60928ea7224152a7e2e1ad4a76cfd9623a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Jan 10 16:35:33 2012 -0800

    moving this

Docs/AdvancedTopics/hopper.run

commit 69c83c282a777dba8826414f760a5db97c08fede
Merge: 46b0ffe 46106c0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:50:28 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 46b0ffeef910e32b93219cf41bf7e2262b559c7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Jan 10 12:48:54 2012 -0800

    cleanup

Src/LinearSolvers/F_MG/nodal_sync_resid.f90

commit 46106c0ea3b1ad86c1dd6c2cdf7e12378203f940
Author: ajnonaka <AJNonaka@lbl.gov>
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 fe0f46152b50b6c41a4e8a17ca1eb6a22a4750cc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3d21a34d7bf26f8cb7fdda269d07bcd7400ae2d8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 919ad433e6506db8ca49f67eb0cc20608a0ec0f7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Jan 9 14:26:40 2012 -0800

    Allow MGT_Solver change smoother.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 6a729c98339eb9035a0dafc364cda5a7c68d58db
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 138a2b186ffe39046d98d25a8471170980c77363
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 17:09:52 2012 -0500

    add bender

Tools/F_mk/GMakeMPI.mak

commit 7cba34de3d61a4788a5455cd8bbae00710c7385a
Merge: cdd044f 5d5e01c
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 15:43:38 2012 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cdd044f6c1879e07bf4c3bf3478bc0718427b2a3
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Sat Jan 7 15:41:36 2012 -0500

    update with separate web directory

Tools/C_util/regtests/Maestro-tests.ini

commit 5d5e01c41e057cfa524c223f816f07471b1ea091
Author: Ann Almgren <asalmgren@lbl.gov>
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 04baf66392cb8a7014a7b7bc415bf80048fcc888
Author: Ann Almgren <asalmgren@lbl.gov>
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 8cba4afff361cfc6ccf5580d3732fe6b208e0e67
Merge: c4690f5 119ce3f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Jan 5 17:21:17 2012 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit c4690f508c9d792b52e1e82807adcd4b56370cdd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 119ce3fe36fc89f560581b7eb327e5a34e548f27
Author: vince <vebeckner@lbl.gov>
Date:   Thu Jan 5 16:10:10 2012 -0800

    added rodan.

Tools/C_mk/Make.mpi

commit 66992034ec62ffcf885be5697f77ab17fbec90b0
Merge: fe2cfa8 1a9bd79
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Jan 4 14:07:59 2012 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit fe2cfa8b1e6c3af8923b6beb673fcdb174ae7907
Author: lijewski <mjlijewski@lbl.gov>
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 1a9bd79938df655d6cf82768a6ce1d917234eed0
Author: Marc Day <MSDay@lbl.gov>
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 3eba53a80224f80ff92d8a6a2234e08b5048bcc1
Author: Ann Almgren <asalmgren@lbl.gov>
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 96a1fa2ea68588544c70edd2ff3174ff1d18e6af
Author: Ann Almgren <asalmgren@lbl.gov>
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 1574e6991d0d6c3dddf2c2a2c20870bc6a9b94b8
Author: Matthew Emmett <memmett@unc.edu>
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 29c238b19bc1c7c7a8259f69207641314b93efc3
Author: Matthew Emmett <memmett@unc.edu>
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 0e7435273168d52f700f3cac9de126068db23f60
Author: Matthew Emmett <memmett@unc.edu>
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 7b9343e21ce0bdc78520817891c1ac8f1aba9509
Merge: 7582693 c8e22c9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 29 12:26:40 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7582693114ff579398527ad8c05c4fc0f978f1ac
Author: Ann Almgren <asalmgren@lbl.gov>
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 c8e22c93ff0d4bf23c87dcc782adbf3c9576d567
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Dec 26 09:51:18 2011 -0800

    Added code for cims.nye.edu for Aleks.

Tools/C_mk/Make.mpi

commit d2a3d2c0a4d7f710d07fd344ccbc396773435fc9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sun Dec 25 17:47:34 2011 -0800

    Remove unused variable in Particles.H.

Src/C_AMRLib/Particles.H

commit af8e70eaef0ec7a6460ff441bf9cbaf78c37ac4e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fc20f9554e6a613930b5e774f6c3fecd8e15a9f3
Merge: 61cf7f0 79acec6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 21 08:49:30 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 61cf7f0af039f04284a97aef300da501155aeaf0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Dec 21 08:49:10 2011 -0800

    Fix defaults for NReaders and NRedist.

Src/C_AMRLib/Particles.H

commit 79acec6c58221eaed8b41ad9a97850d3283abec6
Author: ajnonaka <AJNonaka@lbl.gov>
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 5a1dd1a5df21a855409d3973f556cab9be2fa8d4
Author: ajnonaka <AJNonaka@lbl.gov>
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 0faeb762d0edd3d50fc2b925f2a6c9ae3f229314
Author: ajnonaka <AJNonaka@lbl.gov>
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 b831b864b8b446e6d52efe9dcb2dab9aea656592
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 19 12:20:33 2011 -0800

    clean this up

Tools/C_util/Convergence/GNUmakefile

commit fdac7fee6aa73d9cf77ada046bfaa7d93ff3a5c4
Author: lijewski <mjlijewski@lbl.gov>
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 b3d93cf0fd91df231dc4632b5b09cf11152bf6c6
Author: lijewski <mjlijewski@lbl.gov>
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 27187d63fc3dede4c9e71c2938714c61eca66914
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Dec 14 13:15:09 2011 -0800

    More mods for Gunther.

Src/C_BaseLib/GNUmakefile

commit 3b2937b1c20fc95ef6333aa0acacc5de92bac112
Merge: 694cf96 cc6e151
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Dec 12 18:52:24 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 694cf96dc9050e3daf0cf6a3fc1ec99230cf9a78
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Dec 12 18:51:46 2011 -0500

    fix cray path

Tools/F_mk/GMakedefs.mak

commit cc6e1512f22aa71219a5dc76eed231a517d16005
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Dec 12 12:46:49 2011 -0800

    Add domlo and domhi to interface for ErrorFunc2.

Src/C_AMRLib/ErrorList.H

commit 3576f724d31d963588ae9a5c771f62a413edd0ab
Author: Matthew Emmett <memmett@unc.edu>
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 ec2ebc2be594b79297d6632591984745c83cf867
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2ba36e0b3c83aa0c0cd3fb0c29e0bd7b5f2f3991
Author: lijewski <mjlijewski@lbl.gov>
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 c8adb2db1a31baccc7a7dfd83a9f37fe22702bd7
Merge: 8304758 da53d91
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Dec 9 15:37:54 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 8304758651fec2e56745c4da29c98ab02fb22bd8
Author: lijewski <mjlijewski@lbl.gov>
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 da53d918616a8ba9b71a70f600b2cf406c42c865
Merge: e3a0ebb ae8c47f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 17:25:36 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e3a0ebb3126a0722d2d30705ff6a081dca735427
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 17:25:09 2011 -0800

    undo change in .gitignore

.gitignore

commit 1371f4ea700f54c7ef46df37f5460d517ec7ab1d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 ae8c47fd9acbe8e14645dff16cc7cc25d315ceb2
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 14:56:47 2011 -0800

    Remove defined-but-unused "gridloc"

Src/C_AMRLib/Particles.H

commit 147eef2def11489f58ebc33332d2e61fd80a66b3
Merge: 5ef337a 5e0eb1d
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 14:12:35 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5ef337ae0d3313d2d111752d183ed92b67cbdf61
Author: Ann Almgren <asalmgren@lbl.gov>
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 5e0eb1d7983aa49b34a5bc68dee89af70d8d3348
Merge: 19218c3 a246b88
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Dec 8 13:32:58 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 19218c3a2089dc212de506dc4b67d2e65d28b0c8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a246b88670cda1aeac8b12c61eb92aac4b75ee47
Merge: 484fd0f e15c036
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Dec 8 13:11:35 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 484fd0f2538177c94ce6ecabce4a8f4e477dbc8f
Author: Ann Almgren <asalmgren@lbl.gov>
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 51912ef31a8ff67f8f23b45df2acc907c90d0aeb
Author: Ann Almgren <asalmgren@lbl.gov>
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 e15c03629eb6c7947c98d70682008f4402649a67
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Dec 7 20:21:39 2011 -0500

    pretty it up some more

Tools/C_util/regtests/testnew.py

commit 3f18f2d096ac6083165cdeb8c8858e3abb000e07
Merge: 41002b9 e535678
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
Date:   Wed Dec 7 15:41:41 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 41002b9efb22278fc924644cbabe90fe54cf71f5
Author: Michael Zingale <zingale@bender.astro.sunysb.edu>
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 e535678c02d747735869c199b10f0dc2e32c92e1
Merge: 2016103 41feff8
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Dec 7 00:34:40 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 201610315b191c3f3d3cd29779fd3331cb4fd879
Author: Marc Day <MSDay@lbl.gov>
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 41feff82f0bb14c22efb3cb02a44eeb76691d2bd
Author: Ann Almgren <asalmgren@lbl.gov>
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 244d30baf144caa311689ffcdd5c9fa4a68f15ce
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Dec 6 10:11:31 2011 -0800

    Need to fix NRedist default.

Src/C_AMRLib/Particles.H

commit 6dda459bae7a60af869a3e4ca245a6259a9f9d59
Merge: b47507b 6d32518
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:42:31 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6d32518b3bc58de92bd13eec74c0e84efc261df1
Merge: 49a7872 d94d633
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Dec 5 14:41:57 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 49a787204f2d1a96a98ff498022f77f92c1d8d26
Author: ajnonaka <AJNonaka@lbl.gov>
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 b47507b940c74f30a33221b6a1230d6dff6593b1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 d94d63364d53dd0f693e74414485b87673c83255
Merge: 90ed7e5 1d97652
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Dec 5 14:31:04 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 90ed7e598530073bc7b12071f24fb6e035424f6b
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1d97652020e3a0d14f8f86515596a1278ec4f5ea
Author: lijewski <mjlijewski@lbl.gov>
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 9f199f53eb595e38eaaeb461180eb514a12d3304
Merge: 730d223 37ca7ad
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:11:02 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 730d2234731db401fb934b102e16697d25652d4d
Merge: 91ceeff 05e230a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:08:28 2011 -0800

    Merge branch 'master' of /home/marc/src/CCSE/tmp/../BoxLib

commit 05e230acf801011e50af4a9e4338e42eda4d4454
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:06:46 2011 -0800

    Other part of rename

Tools/C_scripts/gen_release_tarball.txt

commit 0e93aa690c66dc7e3c0da2ac179c10f2f6d3370a
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:06:07 2011 -0800

    Make tarball notes into a script

Tools/C_scripts/gen_release_tarball

commit 91ceeff135f39b7783521930bf9a5e1a55b825ff
Author: Marc Day <MSDay@lbl.gov>
Date:   Fri Dec 2 10:01:56 2011 -0800

    cmake fixes due to Ben Andre

CMakeLists.txt
Tools/CMake/InstallManager.cmake

commit 37ca7adfd0aac3879bd9962051069ce880f50486
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 21:27:52 2011 -0800

    Fix up InitFromAsciiFile.

Src/C_AMRLib/Particles.H

commit aadc1b399dca0c8a79c653e4984e62aef1c97512
Author: Ann Almgren <asalmgren@lbl.gov>
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 449e35083b353dcb1253592bec2f3860b3a5dd62
Author: lijewski <mjlijewski@lbl.gov>
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 bcb93e381fee7756f1957d8eeba545c5ee6c0a65
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:33:20 2011 -0800

    One more int --> long in Particles.H

Src/C_AMRLib/Particles.H

commit bc618d626f20db6c731dc98c1590e5956506cf73
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:32:12 2011 -0800

    One more int --> long in Particles.H

Src/C_AMRLib/Particles.H

commit 98e48cd941bcb89699a93a003a02e66a4827028d
Author: Ann Almgren <asalmgren@lbl.gov>
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 a89fc79a149ed60e3cd506ffaf4bc78c045b8bfc
Merge: 6e713b2 6c4cdf0
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:17:22 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 6e713b2ea3f49f2d23324de21a9e8c822bf604fa
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Nov 28 15:17:13 2011 -0800

    Fix error print statement.

Src/C_AMRLib/Particles.H

commit 6c4cdf0c2fa9ace75a82511f7bfb874a1153db3b
Merge: 8fbe03e 50b273c
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Mon Nov 28 13:59:53 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 8fbe03efc3d6359046c4c054dcb0eb72b066ca2e
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 50b273c43fb19cf6d47c7c879bb5f90c7d7a9e02
Author: Ann Almgren <asalmgren@lbl.gov>
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 907aa4c1ac0892ddddd8cc670e9da35edb4cc781
Author: Ann Almgren <asalmgren@lbl.gov>
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 cbf86e3475f97653e3f917a461fb9b600ee5520b
Author: lijewski <mjlijewski@lbl.gov>
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 12101839f885474cd2bb5ac5752b6e327acd5a1a
Author: lijewski <mjlijewski@lbl.gov>
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 0e98fb6035a69c8bb158af4661605bb3b99a7ca5
Author: lijewski <mjlijewski@lbl.gov>
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 354c12f2f3a503ebc6aaafd66705b641d551b252
Author: lijewski <mjlijewski@lbl.gov>
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 aa2a5bbbf727109f43aa01e87d1d2d517467d7d8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:49:15 2011 -0800

    Fix shifting in domain replication in Particles.H

Src/C_AMRLib/Particles.H

commit 4a8e317dad80946cd090a0e305dd3ac1d70b2260
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:39:14 2011 -0800

    Remove random debug statement.

Src/C_AMRLib/Particles.H

commit 38c2f2269dc67445d5457ce88a1f6dca4142ab2c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:38:11 2011 -0800

    Fix test for print statement.

Src/C_AMRLib/Particles.H

commit e06387da5d83e83b851b15ba057243a17df00d4b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 23 10:35:25 2011 -0800

    Fix typo with lNrep...

Src/C_AMRLib/Particles.H

commit 1998fbdbdcd6dff1ffeff779d9d0160185c22125
Author: lijewski <mjlijewski@lbl.gov>
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 3316244707ed9562ab4abd6930ec0511f028e4da
Merge: 47ea2d1 3c66da0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 23 09:43:26 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 47ea2d18bd6f96ece1cf882524d9bc8ea3c5b7f8
Author: lijewski <mjlijewski@lbl.gov>
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 3c66da0e32d57399982176bc9e87f36b024e9671
Author: Ann Almgren <asalmgren@lbl.gov>
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 b823629eeaef184ef274523ebe90783512fa51cb
Author: ajnonaka <AJNonaka@lbl.gov>
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 adc71bb4e3d0b8a48a21a7b0154d7d3002ccd292
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Tue Nov 22 20:41:20 2011 -0500

    frontmatter page numbers should be roman, main page numbers normal

Docs/UsersGuide.tex

commit b0499e4aa60841b14e2b34eff9d579c79f36c72f
Author: Ann Almgren <asalmgren@lbl.gov>
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 64104cbc58cadabe5bf3c380e700d6d74af647c5
Author: ajnonaka <AJNonaka@lbl.gov>
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 201d08ec73534348fcc8126306bc3cdfffdc5c15
Author: Ann Almgren <asalmgren@lbl.gov>
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 3306205caca4acdc35b6ef7d552a8017f04bf080
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 11:21:25 2011 -0800

    getting started section complete

Docs/GettingStarted/GettingStarted.tex

commit b87bf023c303265ff811464130fb394cbc00bf19
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 10:25:04 2011 -0800

     more progress

Docs/AdvancedTopics/AdvancedTopics.tex
Docs/GettingStarted/GettingStarted.tex
Docs/UsersGuide.tex

commit 2108f2485a5584f02e6f0446d8e3a677c7c2f4a8
Author: ajnonaka <AJNonaka@lbl.gov>
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 dffffeb26fcb6b3326e5d0bd1b6f483f6c7ab7a6
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 08:37:53 2011 -0800

    new section

Docs/AdvancedTopics/AdvancedTopics.tex

commit 13f0096e50c3a7da0e4cb6b78a6de1df85b72093
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Nov 22 08:06:44 2011 -0800

    turn off MPI by default

Tutorials/WaveEquation_C/GNUmakefile
Tutorials/WaveEquation_F/GNUmakefile

commit 6964bb8db84965d3cd4e57d683afff7d6748e150
Author: ajnonaka <AJNonaka@lbl.gov>
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 e0a4d8b53779a07c9cd83a16728b86480a4ae427
Author: ajnonaka <AJNonaka@lbl.gov>
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 b2908d56c1694d55b27d0a7ccaf6aa08b0cb58b2
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 14:34:16 2011 -0800

    new fig

Docs/Introduction/AMR.eps
Docs/Introduction/Introduction.tex

commit 1422087b19b344e076c724de649992488601152e
Merge: d4dccce d01ad17
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 13:40:32 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d4dccce42599d80c2e0aecea03b8d77182e3309e
Author: ajnonaka <AJNonaka@lbl.gov>
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 d01ad1707993eec099a5987b124f85b127d8c25c
Merge: cce69f9 f21d5a8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 21 12:42:11 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit cce69f93485a627a459f888fe41a78fd8b111b01
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Nov 21 12:41:54 2011 -0800

    Mod to compile with PGI on hopper.

Src/C_BaseLib/CoordSys.cpp

commit f21d5a80bec8b0b68d038cdce05d1d7aa21da05f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 11:25:15 2011 -0800

    saving progress

Docs/GettingStarted/GettingStarted.tex
Docs/Introduction/Introduction.tex
Docs/UsersGuide.tex

commit 6bc5dec6d1d1ad2c76926f342f317c2700e3719b
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Mon Nov 21 09:37:20 2011 -0800

    now this builds again

Docs/Introduction/Introduction.tex

commit aa92dcf60c2fa8930168de9696406a7e87b8c5dc
Author: ajnonaka <AJNonaka@lbl.gov>
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 3fa44c6b57cce24a55016b22eecc0c864e88f949
Author: ajnonaka <AJNonaka@lbl.gov>
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 008a0622fbef621a925468b893dbf8f0869804a8
Author: ajnonaka <AJNonaka@lbl.gov>
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 ccf821fc5fbdd87c81fd37b317bb10cb2d8feff8
Author: ajnonaka <AJNonaka@lbl.gov>
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 0bd82fc4b746e534fd99b606dd966fbe8f7f883a
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Nov 18 12:31:43 2011 -0800

    remove unused variables

Tutorials/WaveEquation_C/init_data_2d.f90

commit 97cece503026d5714a5e65ecc6ab5adc77b1d6c3
Author: lijewski <mjlijewski@lbl.gov>
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 60e49e8887c11ef51d1e178c0c5e6c78dd95df33
Merge: 7a134e6 089f349
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:14:32 2011 -0800

    Merge branch 'hypre'

commit 089f3499427013eedae833e5a97045f094e536b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:13:36 2011 -0800

    Minor changes in input file

Tests/LinearSolvers/ComparisonTest/inputs.3d

commit 7a134e64cbb590fed2f7e6a23a3c99cd2bb1db59
Merge: abfa7d6 864b3cd
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 12:12:02 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit abfa7d69aec6dbe9f67cd79fc069a8f1c32e3d7f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 864b3cd1e128f7b1ff40bf96242685197f7b8537
Merge: 533705b ddc99b7
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 10:58:18 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 533705b6e479c651d9f8a75396a80db201b4a07c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 10:58:02 2011 -0800

    Minor performance tweak to copyassoc_check().

Src/F_BaseLib/layout.f90

commit 5bae57425b7c9180063494642751e451e9e1768e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 bfb675fb27f78de40c3b0501e928689a55cfa30a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:35:32 2011 -0800

    Remove a useless statement.

Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit 1b2767e18ffa88317ea7f616901dd983f3f8508d
Merge: 5c81155 ddc99b7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:19:41 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5c81155787a1ef2a5d4ab73fd70ae3524bb05cb6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:18:55 2011 -0800

    Fix typo in a variable name.

Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp

commit ddc99b7aaf280b82b44f45c0662d544879c00d73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Nov 18 10:08:27 2011 -0800

    delete BndryData objects in the destructor of HypreABecLap

Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp

commit 4f4b88299f587d92f658fe6a32b258f9dd4d2e4d
Author: lijewski <mjlijewski@lbl.gov>
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 55f782362f8bba46fa83860367548c9a807eb37f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 18 09:21:27 2011 -0800

    Added -lmpl for my machine.

Tools/F_mk/GMakeMPI.mak

commit 601bcdb325c712f0b3761e29121099cca262f63a
Merge: 5f2a258 30356b5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Fri Nov 18 09:51:56 2011 -0500

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5f2a2582f1823310b4cc78d74b5ef3c80e234ef0
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 30356b5b963010735f14967a428f8375fd63caf9
Author: ajnonaka <AJNonaka@lbl.gov>
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 2d199a1967eaaf4a1242a2e16aea308decb5bff9
Merge: 2edeec8 ded6978
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 17:51:10 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 2edeec88ab457fee5a59e98ef8f186e391c20d0c
Author: ajnonaka <AJNonaka@lbl.gov>
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 ded6978783361298ba77a8b0eace6dcf4f478689
Merge: 155d46f cd1fff3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 17:14:10 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 155d46f78e9a8c17eec103addc48ae1aa26f8b4c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 cd1fff3499060a7600e185870487463d67629f52
Author: ajnonaka <AJNonaka@lbl.gov>
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 ccc53a1e61dbcf007dbfb84e174a168e598fb5dc
Author: lijewski <mjlijewski@lbl.gov>
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 293e74cd2e980fbb6949289c80939a2b009dc3f7
Merge: 7ec0f90 fa7cbff
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:29:33 2011 -0800

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 7ec0f902ddf6a850ad0843e5a1c9e37d394406e5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:29:17 2011 -0800

    more re-org

Docs/GNUmakefile
Docs/Overview/Overview.tex
Docs/UsersGuide.tex

commit 8a864c4beaacd916b7469414ac9d9387ce9afc57
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:24:24 2011 -0800

    new section

Docs/GettingStarted/GettingStarted.tex

commit 878cdfdfc4520f5b536c4c0a7a89e052849e4549
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:23:02 2011 -0800

    re-org

Docs/GNUmakefile
Docs/UsersGuide.tex

commit 8d1f3ae3888833c1c420ae4e59778fb3d393fa39
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:22:14 2011 -0800

    re-org

Docs/Preface/Preface.tex

commit 06baaa3305175f69939b21fedceddb27c8298972
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:21:41 2011 -0800

    re-org

Docs/Preface/preface.tex

commit 769a4c1b27dfdc02fa15d2f63fbdca7813fb0bd8
Author: ajnonaka <AJNonaka@lbl.gov>
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 1130ea23c1b3fdf12bc708218954d12dc29a45d5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 15:20:58 2011 -0800

    re-org

Docs/BoxLib/Overview.tex

commit 2ad363cf5c8788b56211882d18fe7feb65fb5e1f
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 14:52:06 2011 -0800

    updates

Docs/BoxLib/boxlib.tex

commit fa7cbff4834b2d173a6ed8d3bd46473ab0e1808a
Merge: 37b345c c76202d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Thu Nov 17 12:59:37 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 37b345c6f1c0830b1e4014c9d3c838d8a4b18a92
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c76202d098b98506d9d01a78d227a25348bfe97d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 12:19:35 2011 -0800

    updates

Docs/BoxLib/boxlib.tex
Docs/preface/preface.tex

commit 006862404d90c0c5600f12d4a94c0463aa2804f7
Author: ajnonaka <AJNonaka@lbl.gov>
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 fa649f8ce88617eaae6fc24adbfc74eefc30996d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:06:43 2011 -0800

    moved file

Src/C_AMRLib/OpenSource.txt

commit f1b97850e63bbbebc0930d7ebda477185f5e9e83
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:05:45 2011 -0800

    boxlib tree figure

Docs/BoxLib/boxlib_directory_bw2.eps

commit 55dfcaa077aee5485f29cba52e8df62288d7dfc2
Author: ajnonaka <AJNonaka@lbl.gov>
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 6671913aa8d85aa02deb15b314b70bea092e06d1
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 11:04:12 2011 -0800

    moved license from C_AMRLib

license.txt

commit e7c1330b9f52db002dbef832d9e266e57991a0f3
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 10:15:31 2011 -0800

    renamed UsersGuide.tex

Docs/paper.tex

commit 657e80439f7cac20a560187a73f03f57b0c4117e
Author: ajnonaka <AJNonaka@lbl.gov>
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 af4064da45d071b3d64a408dffd5317c29a9d802
Author: ajnonaka <AJNonaka@lbl.gov>
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 68e80a8d6a16c2530ad915a9378cd4a4cf029543
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:27:24 2011 -0800

    git rid of these too

Docs/BoxLib/mac.odg
Docs/BoxLib/mac2.eps

commit 82b0ed43eb89b24ff7d0aa06f140465cd3a60fcc
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:24:39 2011 -0800

    get rid of this too

Docs/BoxLib/maestro_directory2.eps

commit f7451f0e101526236c0b87a0d9369e54ddc8255d
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Thu Nov 17 09:23:27 2011 -0800

    no idea why this was here
    Z

Docs/BoxLib/paper.tex

commit aadd3b5703cc2bc8325627cfeaf6519f257e3c22
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Nov 17 07:44:42 2011 -0800

    Just a little code rearrangement & reformatting in InitFromAscii().

Src/C_AMRLib/Particles.H

commit e17396dd7fe08ceac8750f8b24c00edd67ca6382
Author: Michael Zingale <zingale@xrb.astro.sunysb.edu>
Date:   Thu Nov 17 09:18:38 2011 -0500

    add xrb

Tools/F_mk/GMakeMPI.mak

commit 3d736e90138b35e6cd3f883ad68a64ef2dfeda3c
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 022a0ec15214e5f07c3ed2adcf2f46b6bd4e9181
Merge: 5d2e733 e560e40
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Nov 16 18:16:06 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 5d2e7336d0003600f58caa6c8b197f54c053fc55
Author: Ann Almgren <asalmgren@lbl.gov>
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 e560e401c33ab8a3b48d2107c7f4988354d53f6d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 16 16:19:32 2011 -0800

    A little optimization & cleanup.

Src/C_AMRLib/Particles.H

commit 9a6c8131fba941cc9f30ae5b81652083a35191ba
Author: Ann Almgren <asalmgren@lbl.gov>
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 0316344b00f4a1e148be64efe28c8c9e05a52588
Merge: bf7f4df b31073d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Nov 16 10:52:57 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bf7f4dfc4592b24910f296e8cfecfeff15caf056
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b31073de0c62326bcea7ae932596e0d78dbdcbc0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Nov 16 10:25:02 2011 -0800

    Removed some unused variables and some prettification.

Src/C_AMRLib/Particles.H

commit 656dfc9fd29ed3a46420d7c30635a9f96e2f309f
Author: vince <vebeckner@lbl.gov>
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 ed89732db8067ff6403f7a960a366c1c197c8dca
Author: Ann Almgren <asalmgren@lbl.gov>
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 1b0c380933a88f9a58c1d0469ededd4c3aca7f8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:30:14 2011 -0800

    untrack tag files

.gitignore

commit 8872f0853150ce375a7219e06a7308d0fdd1cd3f
Merge: d386485 4c6336f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:27:38 2011 -0800

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d386485ff77954e160f2417db507acc6db81a2f0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:23:20 2011 -0800

    Add 1D case.

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 6dec8a2c5d3d30f424905e8afb43542aa02241ef
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 eceec14553c3c61803d807f475d77cab55c7ec6f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fdcb893436be392fd5a4f61d867dd99971acf179
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Nov 14 10:15:41 2011 -0800

    Add 1D case to mg_tower_print.

Src/LinearSolvers/F_MG/mg.f90

commit 9a9495624d6ee89127443adcbe6b82356eb8265a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 4c6336fea97a0e761674ea3a3e917f3af692c53d
Author: Ann Almgren <asalmgren@lbl.gov>
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 bb82920ab1f81b71b389c341b1a7eeadbd1784b7
Author: Ann Almgren <asalmgren@lbl.gov>
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 3dcd64acd92fe836e30c04359d42d8218cf20b67
Author: Ann Almgren <asalmgren@lbl.gov>
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 230fb283cf1ef7158fdd05876054740ea569a777
Author: lijewski <mjlijewski@lbl.gov>
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 b1211ea2ed028adfd3c97d32d2bb72a6f4684650
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 15:07:26 2011 -0700

    eps from 1.e13 => 1.e-13.

Src/C_AMRLib/Particles.cpp

commit 80035b495101ffb45ef552a5a78a084ee78140aa
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 10:31:33 2011 -0700

    Made some loops more memory-access efficient.

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit 36f7f9e22b20fb0fb26ec28c67347505f3da4428
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Nov 4 10:15:12 2011 -0700

    1000.0 => 1000.0D0

Src/F_BaseLib/interp.f90

commit f5fbadb6baa1d499a45ae5a1bbde7de3965632d0
Merge: e599100 5e222f9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Nov 3 22:12:15 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit e5991002f95bd600704cba1eea64d93c8377535d
Author: Ann Almgren <asalmgren@lbl.gov>
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 5e222f906f1b8e7168fcb8fc6477ba59ee3a6a76
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 4dc8453e16dcfa854e6416d6acb2efc9850d4f93
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 0caab601bed3862e92b67d8c91422fc3dc234e4b
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 19:44:06 2011 -0400

    add comments

Tools/F_scripts/findparams.py

commit b4bf17e1bcd2085ba64b1cef1023166e3f804496
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
Date:   Thu Nov 3 15:53:02 2011 -0400

    slight prettification

Tools/F_scripts/findparams.py

commit 729986137648a21b5208db8d0fa936d85445764d
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 4b33ad937d49eb8747147998fad26ea33d6c53cd
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 4583135213e2cb1ce9d85a0b79d41799995e17ab
Author: Matthew Emmett <memmett@unc.edu>
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 4568b590dd5df866b555202cc0afa3a6a61f95a9
Author: lijewski <mjlijewski@lbl.gov>
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 03380a3099bb47f4aed6cd6b6b99563937c881ae
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 28 08:53:21 2011 -0700

    A little note explaining why this directory exists.

Tests/LinearSolvers/C_CellMG/dumpi/NOTE

commit 8f833d714f383cd92575e940f1b8bc00d831ea3c
Author: lijewski <mjlijewski@lbl.gov>
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 648d13ab7df788a163f952f3b62a5e8e5f555dff
Author: lijewski <mjlijewski@lbl.gov>
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 2f03144be46c9d5bd45a0cbb022e6bbda00ab07e
Author: lijewski <mjlijewski@lbl.gov>
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
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 e40aec28e6bbf4c76b760e1f2c2c711837eb83b1
Author: lijewski <mjlijewski@lbl.gov>
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
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 d38d9856c7a863fae3c51f51d69357d22ad2ee95
Author: lijewski <mjlijewski@lbl.gov>
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 3f693e5b7912a48a7a6d09978d674321a96686a7
Merge: 86c7e69 73eb598
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 15:35:03 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 86c7e69aaf677defc37a081ec446d05a4786a932
Author: vince <vebeckner@lbl.gov>
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 cb48ec6e773ceb223324a26e6cea4349442211ab
Author: vince <vebeckner@lbl.gov>
Date:   Wed Oct 26 15:25:57 2011 -0700

    fixed boxlib path.

Tools/C_util/Convergence/GNUmakefile
Tools/C_util/Statistics/GNUmakefile

commit 73eb59861af4433b9054c7e8dede0d579e2ce47c
Author: Ann Almgren <asalmgren@lbl.gov>
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 7c569c28436be896601316de4d5ecb55c8e02657
Merge: 34d014f 988925f
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 14:01:48 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 34d014fb151b9e8ef3ae1b666c0e3ab5dca0e200
Author: lijewski <mjlijewski@lbl.gov>
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 35c8f0f67b4da689b2bf5fde54764f03addad11e
Author: lijewski <mjlijewski@lbl.gov>
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 988925f7d3ae669b1121efd2c75abc7b2f086c56
Author: Ann Almgren <asalmgren@lbl.gov>
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 ee552ff4374df9eec96d0347a40f5f39bba8ee30
Author: lijewski <mjlijewski@lbl.gov>
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 2803d5f6b4819acc0d91b75d16238b2393b9f6b9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 12:22:59 2011 -0700

    Add t/ to ignore list.

.gitignore

commit acc172852ef671997dfc67609e87002b404dea81
Merge: afbce3a 42e5f79
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Oct 24 10:42:50 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit afbce3a60fb36634736695e11a2620bbde6ca037
Author: lijewski <mjlijewski@lbl.gov>
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 42e5f79d8fbc4eb577980fcc54100bdd8aafeac2
Author: Ann Almgren <asalmgren@lbl.gov>
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 1a7d04f042c3793081e06bdcfd9467b7c4f4a991
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 15:57:38 2011 -0700

    Modest speedup to simplify_doit().

Src/C_BaseLib/BoxList.cpp

commit 4c30fa0db73b55d00995383ff984c9b5ec6b4db3
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 14:44:20 2011 -0700

    Got MPI working on my upgraded machine.

Tools/C_mk/Make.mpi

commit 8418c17e843c0fc93fa44aedc4ca2c868cc7a7f6
Merge: 2fafc8a 110e38e
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 21 13:56:20 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 2fafc8abdee5be08b72b287638a618d988a67b12
Author: lijewski <mjlijewski@lbl.gov>
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 110e38e50d3c9599b83b70bc3100e16edae38c6f
Author: Ann Almgren <asalmgren@lbl.gov>
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 b3906daa5ccf835f882fd0651ac35a881b1e7a94
Author: lijewski <mjlijewski@lbl.gov>
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 6b4e094845656d5aadf5216e4621822efea65abb
Author: Matthew Emmett <memmett@unc.edu>
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 d95fd5c7e0af6c32b01c387e264f5d06c85a0840
Author: Matthew Emmett <memmett@unc.edu>
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 bcfb7b58576bfd735e6ea02a5f570a9b72fd445e
Author: Matthew Emmett <memmett@unc.edu>
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 5a34bbe8b48e6fac6d1f79a80d6277b2c0e75a54
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 19 19:27:05 2011 -0700

    Add options for Zarija's machine, stribog.

Tools/C_mk/Make.mpi

commit a2fe501abf74b4a06a99a0b1b8009e55e1320c65
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Oct 18 11:28:19 2011 -0700

    Add a space to the ouput message

Tools/C_util/regtests/testnew.py

commit 537419220029d0d441484ae6e18943f96dcaf67c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Oct 17 14:20:41 2011 -0700

    This has latest greatest InitCosmo from Jan Frederik.

Src/C_AMRLib/Particles.H

commit 35bb875236768e7dc6ee7ad79d84fae9a8117cca
Author: gilet <cgilet@lbl.gov>
Date:   Mon Oct 17 12:27:53 2011 -0700

    added -lmpl for orga

Tools/F_mk/GMakeMPI.mak

commit f5318cd38a6c967623e607b37423b5de4727e0a8
Author: Ryan Orvedahl <orvedahl@sn.astro.sunysb.edu>
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 d44483341d681b9d4a2afdcf8a87f1b8c4eab750
Merge: f6a4cda 1646254
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Fri Oct 14 15:12:40 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit f6a4cda91231f4efc5d397597af2c7b37d506f0a
Author: Michael Zingale <zingale@sn.astro.sunysb.edu>
Date:   Fri Oct 14 15:12:06 2011 -0400

    add MPI stuff for sn

Tools/F_mk/GMakeMPI.mak

commit 16462549dc5c0c3255510d5a69de51e175dc8df4
Author: Ann Almgren <asalmgren@lbl.gov>
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 e3960aa58fbc39a03d46af4e2550f97215a9c4fc
Author: Ann Almgren <asalmgren@lbl.gov>
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 8571c67fd2f6e3f2fd2c68e16a039af9356471a8
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Oct 14 11:34:39 2011 -0700

    Fix mpi for manda.

Tools/C_mk/Make.mpi

commit 7b0fa08efc81d39d9bad37b0da8ca5b761119ad2
Author: lijewski <mjlijewski@lbl.gov>
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 207606d4c205a8d0cc1f9f7ed45860fd4b3a89a9
Author: lijewski <mjlijewski@lbl.gov>
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 aed2c69cfe2ca8b3fe2e2d72ddf1c79789573bdb
Author: lijewski <mjlijewski@lbl.gov>
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 aed3a358951146e68b40a9f21c08baaa18f69353
Merge: 200a8b1 2c38d08
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 12 13:54:36 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 200a8b17ec39e705a3c697f5b7f485134f91ca4a
Author: lijewski <mjlijewski@lbl.gov>
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 2c38d08674fdc983d9493d00c70c96bb97b56722
Author: lijewski <mjlijewski@lbl.gov>
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 9199eccc7efec74c64f1b95a047ccaefd2b44aa9
Author: lijewski <mjlijewski@lbl.gov>
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 b8851cc9682eebaeb22e8466350b013ab625ce11
Author: lijewski <mjlijewski@lbl.gov>
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 ecfcf1e544ed3ad8acdca615f7b3b214ab3d535c
Merge: 0ce3704 7c22d5a
Author: Marc Day <MSDay@lbl.gov>
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 0ce370416a3dda399d6bcb5b628faccaf1c45005
Author: Marc Day <MSDay@lbl.gov>
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 7c22d5a0c6c6e68069650861c48bdb59e9d8e215
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Oct 7 15:59:15 2011 -0700

    std::snprintf() => snprintf() to get to compile with PGI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 44ff6a3c4815f4511add42f354631eb6d3dbbc5b
Author: lijewski <mjlijewski@lbl.gov>
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 da9a293b5800a1f870b406aca9c5128620d14e3d
Author: lijewski <mjlijewski@lbl.gov>
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 3d907e46e81d9121e9296effbdf26a840fd91abf
Author: lijewski <mjlijewski@lbl.gov>
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 e32a61ceb6c82272573308b8dd484a1566e83c20
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 250a9d19d46ae3e77e6f2b183beede879917ec1e
Author: lijewski <mjlijewski@lbl.gov>
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 407404a044029c0b360b9d8bbbd22ea5e0397648
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Oct 6 12:40:52 2011 -0700

    Instead of just calling std::list<Box>::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 c06be835b829a81d4aae78ae6194c6997c3dc6fb
Author: lijewski <mjlijewski@lbl.gov>
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 3e161ca704c5da15ff0eb7da7969526065934a9b
Author: lijewski <mjlijewski@lbl.gov>
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 3b67bea29d3e7c86b1acc296763aa321f4784272
Author: lijewski <mjlijewski@lbl.gov>
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 92fdbc84a1883ecaa28d4de00f400e2837042b76
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Oct 5 20:03:05 2011 -0700

    Changes to InitCosmo in Particles.H only.

Src/C_AMRLib/Particles.H

commit 686858aefbd4a8c6365aef956710b74d99e94821
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Oct 5 16:15:48 2011 -0700

    A little tidying of for() loops.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 1cd4a272cc41ab48bc7a0fbae9fe3091d943f292
Author: lijewski <mjlijewski@lbl.gov>
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 0e6794b3406cd17f4ac3052dbce268311896c42c
Author: lijewski <mjlijewski@lbl.gov>
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 cb37f8b376d63ad0dec758844e91052c74275c17
Author: lijewski <mjlijewski@lbl.gov>
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 a37264280e7fdf157ec86081d057c26be1b8e09c
Author: lijewski <mjlijewski@lbl.gov>
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 d97f643e7850ea4b3fa27c5de84c2a70dc88dfdb
Author: lijewski <mjlijewski@lbl.gov>
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 04aa6ad8c9ee929a213eb03cc3a83dcb8898d84e
Author: lijewski <mjlijewski@lbl.gov>
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 821166294c9aec067dbe61315c3bdc506d08755b
Author: lijewski <mjlijewski@lbl.gov>
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 f2b7bcd0196bdb1e1eedc55990ec810c5329f5ce
Author: Ann Almgren <asalmgren@lbl.gov>
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 42e1b952c138cfb5626957ca604174d5436dfc10
Author: Ann Almgren <asalmgren@lbl.gov>
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 d3e62e3f886b01f87c118d09e3fe228b02721ce8
Author: lijewski <mjlijewski@lbl.gov>
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 876ea658026ee908442bff770e6b105fd4558375
Author: lijewski <mjlijewski@lbl.gov>
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 df144986a1811ac7b8a4f0c0b2c9bbf8aa951185
Author: lijewski <mjlijewski@lbl.gov>
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 15ca7d7db8fd6420703f96ff9ef6266bdcf612d8
Merge: 39537a8 f6ab0d9
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 30 11:43:25 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 39537a80834f6a1eaf6c42efc1fd50b493299d6e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f6ab0d9014c9b4fa430c32de33c5b5f63d131498
Author: lijewski <mjlijewski@lbl.gov>
Date:   Thu Sep 29 16:08:02 2011 -0700

    Quiet compiler warning.

Src/C_AMRLib/DatasetClient.cpp

commit 3276cf0c8be88ac08522ca79f5f81546af8e75e5
Author: lijewski <mjlijewski@lbl.gov>
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 171f6444f686e6ff269ff01ff18866aa6e7ecdd2
Author: lijewski <mjlijewski@lbl.gov>
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 d971268f105b47536662e1b8d9bbaa86e356c342
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:48:15 2011 -0700

    Oops. Forgot a semi-colon.

Src/C_AMRLib/Particles.H

commit 0775ec172e43c6647c6697939f59172b3cdf4a5f
Author: lijewski <mjlijewski@lbl.gov>
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 a5f3345328158031d47fe4f7086086c36e4b97eb
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 15:40:11 2011 -0700

    Cut at new GNUmakefile for GIT.

Tools/C_util/Statistics/GNUmakefile

commit 99413d31bb6c2830dab7b204ec7a9aae859af037
Author: lijewski <mjlijewski@lbl.gov>
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 b2a1bb8d2ca590317c02b5454d391223074abc72
Author: lijewski <mjlijewski@lbl.gov>
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 3a91b0e2266d899b8278c741fb0142e96b4834e0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 28 14:56:14 2011 -0700

    Removed some unused variables.

Tutorials/WaveEquation_C/main.cpp

commit 090fe46083ee54d0a5de9b2d7a9ce9937197e490
Author: lijewski <mjlijewski@lbl.gov>
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 7d09ccf29d04579abeebd067f17eb86ece9f3f20
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 a62ff46c318be5d6b2871db98edc50f0f2d7d3b2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 16:12:01 2011 -0700

    MGT_Solver::set_vis_coefficients(PArray<MultiFab>& aa,
    			     Array<PArray<MultiFab> >& bb,
    			     const Real& beta,
    			     Array< Array<Real> >& xa,
    			     Array< Array<Real> >& 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 27563b647757f05150ca53509cee36671b4f1f94
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6b6b106f0ddbcb57745ccb02952256cb1c8df797
Merge: 3c06599 bc9613a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 14:21:39 2011 -0700

    Merge branch 'boxarray'

commit bc9613a7c6b31b4770bb78573c83a74064b61d16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 3c06599753845035bf17942ed4fa4e84a4693c68
Merge: 0c00d87 af836b0
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 14:02:34 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0c00d87b48c4758a30569954448e768c9f1fb405
Author: lijewski <mjlijewski@lbl.gov>
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 733901080ac93bb9d83716ecc46d20dc795a9cb8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 27 13:58:53 2011 -0700

    Removed some new/deletes and replaced with Array operations.

Src/C_AMRLib/TagBox.cpp

commit be03abf3dda7dd16595e976faf12fa9e6ac65ca1
Author: lijewski <mjlijewski@lbl.gov>
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 af836b0a489897f67f5c89584f14e6ee99813b6b
Merge: f31ffcf dc23a56
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:49:41 2011 -0700

    Merge branch 'master' into boxarray

commit f31ffcf0ac3147899392a51f3393aa3e54d5df5a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:48:23 2011 -0700

    a file containing calls to BoxLib_F

Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp

commit dc23a56a4d009898dff0af54b5c2be1bf8db2a86
Merge: f742182 b13e4c3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:37:10 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f742182099fe785f7f1aa1201f37596041ec7839
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Tue Sep 27 12:36:50 2011 -0700

    write plotfile

Tutorials/MultiGrid_C/writePlotFile.H
Tutorials/MultiGrid_C/writePlotFile.cpp

commit 3118d92daa0bfba6d527a0d54b6398b8f50d2e58
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b13e4c3eddd17416ae3b7311184b5c2fce706443
Merge: bf0450f c206b93
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 27 08:55:49 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit bf0450f99ace578ddd3c136dc8a6b6b3cb4b57a8
Author: Ann Almgren <asalmgren@lbl.gov>
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 37b13c074e2854e97c9e34256cc559bc8acc2d57
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 c206b931582659aa1ad93b9403ae675eb2c3bc3f
Merge: 911058a 5fa0742
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Mon Sep 26 15:55:59 2011 -0700

    Merge branch 'master' into boxarray

commit 911058ab0281d101ad182e3f0f5a424d66bf219c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5fa07424f076b657e186014221cbc84c0fa8a4b4
Author: lijewski <mjlijewski@lbl.gov>
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 3af755e10172e50145c71bf03a2087aa35090c50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 89082af8d0737c0a7b3708ac1a3eac331d71c26f
Merge: ce22154 84b153a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 23 10:15:21 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ce22154867b7cacf0f7596b7867df227568b9a68
Author: Ann Almgren <asalmgren@lbl.gov>
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 84b153aadbcf819c5af970512b735a743232bb8b
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 dd1159cf6982401e59c56a8ffbcebe265969ae3a
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 0ba92b526653a6d1498d0037197b147729bd80fb
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 22:42:45 2011 -0400

    update for testnew.py

Tools/C_util/regtests/Castro-tests.ini

commit dd06551709d4e6c1ec9a3abaa69bd272bdbc6437
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 15f0c8b5fb2b99e8a72c8141493a2fc9781b1928
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 7069ca493547eaaed4afc00d63ac61b7c8bddd7a
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 5f10bcc6c9dba744f917bf65741cdee8b9f80a8c
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fa0f122ac50f50dc941d007173ff1066bf89eb77
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 0ae1f0f4c80a1b2ed7152d2d01375c36905b8db3
Merge: c9129be 481abb5
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 15:20:44 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit c9129be8fd3c8ee6f78973f5798d81e4cbd73c40
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Thu Sep 22 15:20:00 2011 -0400

    add more checks

Tools/C_util/regtests/testnew.py

commit 481abb5297a5f40fc6ee84a2eaa2bfd5391658f2
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 6b6fae2d8871b42df6e0bdbd75bb71010cdd0e0f
Merge: a14094a 1c45040
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:56:53 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit a14094a20e02573dad55dfa809d3f159c8df2fe8
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 7986da139a58e7f5fef6a868cc836ae90fa7243e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 21 15:52:49 2011 -0700

    delete a space in write(*,*)

Src/LinearSolvers/F_MG/itsol.f90

commit 357760719d39ac86d3ba741beb698669fc70c7c7
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8ebfb8b1195c1f86df0978311f1bf1606a5709c1
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 1c450406f5cb4093a33859f47d1ef33706dc13f6
Merge: 5412bd7 ee97988
Author: Aleks Donev <donev@courant.nyu.edu>
Date:   Wed Sep 21 17:26:17 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 5412bd75b4a7764573f3f66ff351ef40478ee7a1
Author: Aleksandar Donev <donev@donev.cims.nyu.edu>
Date:   Wed Sep 21 16:28:33 2011 -0400

    Added Courant systems to Makefile

Tools/F_mk/GMakeMPI.mak

commit ee979881f4b91e0c1d1d48f6305f75b448f3036f
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 a03fc3fa757170c3d071e8b29f8621e9761ad17b
Author: Michael Zingale <zingale@nan.astro.sunysb.edu>
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 5256c0efea8efc4c6220d90034a215abf48999d6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 95473e2fcfcf26e63d44fcd9c52e5b093ed57cfb
Merge: 27393a8 446a5db
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Sep 19 17:19:18 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 27393a8a43599e1ea363cb764e0338dcdc6519cb
Author: Marc Day <MSDay@lbl.gov>
Date:   Mon Sep 19 17:18:55 2011 -0700

    Replace Wall with everything but unused-dummy-arguments

Tools/C_mk/Make.defs

commit 179de187e7c91d3c984ffe8705c5fc4e72e68576
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 446a5dbfaeed6eb6b7cdf31bf535d5648a62cf88
Merge: 4bb5994 cb8b4bb
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 19 13:50:40 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 4bb5994a294d8b72b09b418b5004e387303a076f
Author: Ann Almgren <asalmgren@lbl.gov>
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 cb8b4bb81fadb4c58299486e7aff7bf6d2ef7e35
Merge: 7f9dd74 d959e2c
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 19 13:07:46 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 7f9dd74f852a11cdfefae5cb6e371eafb2238ff8
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 19 13:07:14 2011 -0700

    Some endian test stuff for Darwin from Chris Malone.

Tools/F_mk/GMakedefs.mak

commit d959e2c9468a6ddf544563c719198229b33384b4
Merge: 9826b58 fc45630
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
Date:   Mon Sep 19 15:22:40 2011 -0400

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 9826b5873bb60d2ac306d1a8d1892ff14e27ab2c
Author: Michael Zingale <mzingale@mail.astro.sunysb.edu>
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 fc456301f8bfc758f8b1fae3dae6cd88dbd9ea80
Author: Ann Almgren <asalmgren@lbl.gov>
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 f561c5cce488d3de6ffd341bcc6fb867cb66229f
Author: Ann Almgren <asalmgren@lbl.gov>
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 09871e7de3592b21763be1afc1a485c75a5251a5
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 18:27:38 2011 -0700

    Add new flag to control BoxLib_C convergence criteria.

Tutorials/MultiGrid_C/inputs.3d

commit 31436522175714c49ac0474a116d31a4135dcfa3
Author: lijewski <mjlijewski@lbl.gov>
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 ca1131291f1159b687a11ee2bd872563a7b219c8
Merge: bd7f979 8a5c813
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 16:19:56 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit bd7f979dd84f5393fede8f92c84f12c236df5cc5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 16:12:54 2011 -0700

    fix a problem in inputs

Tutorials/MultiGrid_C/inputs.3d

commit 8a5c813050fc481c50e4d78a6c54b39db706c19a
Author: Ann Almgren <asalmgren@lbl.gov>
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 3771253dae9c1537a2aff7d02bb365b1083c8317
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 15:26:15 2011 -0700

    Fix test for print statements regarding convergence

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit b866af072ceef9b4033a98e239a0a5edb53a08db
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 16 15:04:57 2011 -0700

    Clean up print statements for convergence test.

Src/LinearSolvers/F_MG/ml_cc.f90

commit c992133785f25a9a6cf4ddd016c82537aa01a163
Author: Ann Almgren <asalmgren@lbl.gov>
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 2f9a7a5d3f14209d15f5e566f9b454667d0a62db
Author: Ann Almgren <asalmgren@lbl.gov>
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 904298f01c8a13af7670a17bfb8a810208be720e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 13:13:06 2011 -0700

    pass high-order boundary parameter to Fortran

Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F

commit 2cfd0849953447c836351af2906d8b3d851b2f16
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 57bb6e98e68b969c5836f0ffcf8e328da719a18d
Merge: ef8caae 2c203da
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:45:48 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ef8caaee1209bb26c7c2ecd2b9fb61053d7a97bc
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:45:40 2011 -0700

    minor cleanup

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp

commit db8bff7285e0f202952a308fd6b2998cd32fb510
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Fri Sep 16 10:44:38 2011 -0700

    remove redundant soln.setVale(0.)'s

Tutorials/MultiGrid_C/main.cpp

commit 2c203da574e99842e883d336571a88f654df3d1c
Author: Ann Almgren <asalmgren@lbl.gov>
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 77022ccfc18c1b77d2a934c4d44eedf1fbde2e57
Author: Ann Almgren <asalmgren@lbl.gov>
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 148b6fc19287bc6772ff2cde0b1317ff76163407
Author: Ann Almgren <asalmgren@lbl.gov>
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 11bd7dc0d3c9067dfa63eeac1e1062f72a5da50f
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 fcff860f9bbc763877f704a838bf069826c9c68a
Merge: f37c154 402c450
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 f37c1548ac30085748d55bcd39d17e43f14c93f5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 402c4507d933431fac2bcd665e1358845899bef5
Merge: 1fd6890 ecc71f6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 15:35:43 2011 -0700

    Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib

commit 1fd6890c30f350463a623ee4eefba32b26b48c77
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Thu Sep 15 15:35:25 2011 -0700

    Add solver_type = "All" and additional print statements.

Tutorials/MultiGrid_C/main.cpp

commit ecc71f63e99cf75674b1445a976507f2252eb253
Author: Ann Almgren <asalmgren@lbl.gov>
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 9ab21bd28a9639164ad3331b006a495cbf0d17aa
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2eff9b880d0582abd6d81445d352183c668f3ec0
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 8769abc6e192ab13ae63087ffc27dc428f7f2970
Author: lijewski <mjlijewski@lbl.gov>
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 9d66dd2a2d6925fb7baaa4d68e8f2cab7a72c999
Merge: 0fca70a 21ab65e
Author: Marc Day <MSDay@lbl.gov>
Date:   Thu Sep 15 08:46:57 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 0fca70a5b852b6c620952ef8eaf3b6c00987a5d4
Author: Marc Day <MSDay@lbl.gov>
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 21ab65eacd01206899e8be2512ec23c3dce655c3
Author: lijewski <mjlijewski@lbl.gov>
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 6cc3450aff163bcae028488be5b6a18dd0a07a78
Author: Ann Almgren <asalmgren@lbl.gov>
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 ca596ac233c710651f857ff41e328fde28e28ab9
Merge: 064e854 e5d1f1e
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 18:20:48 2011 -0700

    merge

commit 064e8540f8a9071d1641485c11a542583af09ab5
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e5d1f1ef29f8e083f8f35b51119773e87d5db0a5
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 14 17:11:11 2011 -0700

    More mods from Chris Malone.

Tools/F_mk/GMakedefs.mak

commit b303351e9b19db103b2cbb9a6aeca0a0e17d86f4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Sep 14 16:51:48 2011 -0700

    Added Darwin_intel.mak from Chris Malone.

Tools/F_mk/comps/Darwin_intel.mak

commit 54caef468b819921d73cbb8ab41534ee7994a68a
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 14:19:49 2011 -0700

    Add comments about verbosity flags.

Tutorials/MultiGrid_C/inputs.3d

commit e251f094cadddc0c34becdfb6e6651b99a95d7c6
Merge: 55af7b1 9cf4e46
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 13:29:35 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 9cf4e460a1bcbe76be002aef78d640d3b3c22408
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 12:51:39 2011 -0700

    fix default BOXLIB_HOME

Tutorials/MultiGrid_C/GNUmakefile

commit 899f5b6917608215cd010e06254bbd7bf827150d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 e9e21416bc4ca8e54c79ccb6294422071023af50
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 10:19:25 2011 -0700

    add the iostream and iomanip headers to HypreABecLap

Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H

commit 59b01e5a147a01c47e62d12bcc827d876e78fe73
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 55af7b1221be96e984d2aa37a62de9eb0361cd1e
Merge: 2842e2c d7f4e73
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Sep 14 08:29:26 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d7f4e737de464fba0b0e169d9268c39d64c921a6
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b384a47ac9d3f362b15b045b478f41cd74bfb8e4
Merge: d0d2fcb dbd51e3
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date:   Wed Sep 14 05:38:55 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d0d2fcb338e4c6f9d94d1a1174770588d1d2a59d
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 2842e2cdec5d82c12418057e5e9cc4fc1bc7f069
Merge: 433581d dbd51e3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Sep 13 22:08:12 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e0e6504fe7aad096d52907c2771fa62a43b63916
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 dbd51e3ba2a46a7d030f34b022de89c025f15272
Author: Marc Day <MSDay@lbl.gov>
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 433581d40ccc2ddc75132bb4051ac2513962c758
Author: Ann Almgren <asalmgren@lbl.gov>
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 a52c141bdbe3a50962fc9935ec113aa719d9abb6
Author: lijewski <mjlijewski@lbl.gov>
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 22b9473cd7a908cfac60d6c4ca6613169c16721d
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Sep 13 10:51:34 2011 -0700

    More work on parallel copy test.

Tests/C_BaseLib/tMFcopy.cpp

commit fe5d610e70e86b194533390cf97c5c6a91ac30ff
Author: Ann Almgren <asalmgren@lbl.gov>
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 335d2fb1d0aed573b63ee17f7c35a20138464a04
Author: Ann Almgren <asalmgren@lbl.gov>
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 7c6b42a61a5dd3382b041633acc2a2a61a788842
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
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 b347a609d3d8712efc4eccbe332b3477fcf4890a
Merge: ec0a883 33413e6
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 14:53:52 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit ec0a883e7a0364095da0cbd0545c427d5f6f2b7c
Author: Ann Almgren <asalmgren@lbl.gov>
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 33413e65cacbdbba82379bee4bea4bb3eb739357
Merge: e6dcb17 5beed29
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:31:11 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit e6dcb173b2ea6bae3e3c12454ebb0f04bd582b96
Author: lijewski <mjlijewski@lbl.gov>
Date:   Mon Sep 12 14:30:59 2011 -0700

    Fixed typo in comment.

Tests/C_BaseLib/tMFcopy.cpp

commit be6349c1429cd137a6ed7fabba39d4e602ab5f4f
Author: lijewski <mjlijewski@lbl.gov>
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 8ac97f486cc1ca2e10874f1e227a2a0a539616cf
Author: lijewski <mjlijewski@lbl.gov>
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 5beed29d65613c0aeaa61cafb52d9ebc341c248b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Mon Sep 12 12:55:35 2011 -0700

    Remove extra arguments so this compiles.

Src/LinearSolvers/F_MG/cc_stencil_fill.f90

commit 98e04d0b35240c803d55d99588b89b5c3ba7c9b9
Author: Ann Almgren <asalmgren@lbl.gov>
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 c6d6896b276b6fbe4d5b03fa7eb1b19ed646f31d
Author: Ann Almgren <asalmgren@lbl.gov>
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 e14967c1f6355a9009577f3856e4918b64a8a9fa
Author: Ann Almgren <asalmgren@lbl.gov>
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 28ce486a549cd6bf0e767b9ac081e40a1871cbff
Author: Ann Almgren <asalmgren@lbl.gov>
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 c029a76578d71a39ee8220d33af09e3f56c29105
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Sep 9 17:25:13 2011 -0700

    No need to copy mf into plotMF

Tutorials/WaveEquation_C/writePlotFile.cpp

commit 2d1f88296b3e39250040e3b68f7881cf037719b9
Author: Ann Almgren <asalmgren@lbl.gov>
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 <asalmgren@lbl.gov>

Src/F_BaseLib/mt19937ar.f90

commit b5982ce6397f962f60c80d995ad18d461d476892
Author: Ann Almgren <asalmgren@lbl.gov>
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 1f976bf6558eb1b54f1ae7c9c80121668d78ac20
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 19:15:59 2011 -0700

    version/release info

BoxLib_Version.txt
Tools/C_scripts/gen_release_tarball.txt

commit c4ce57b990c33b57b0a721cd8b584d5952ab5175
Author: Marc Day <MSDay@lbl.gov>
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 bb0c52ff2653fac67f9ab057189935478368ab59
Author: Marc Day <MSDay@lbl.gov>
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 8ed8f3c60b7f4f9cb4eebaebf4a4cf3f38156417
Author: Marc Day <MSDay@lbl.gov>
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 317490ddfd150c21486b3de05c3d046e68f2c462
Merge: 41a2e68 ea561a2
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:34:43 2011 -0700

    Merge branch 'master' of /home/marc/src/CCSE/BoxLib

commit 41a2e68432f6483b50f90e74f95dd3d02842e6da
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Sep 7 18:32:09 2011 -0700

    Add Utility.H

Src/C_AMRLib/SlabStat.cpp

commit ea561a2c1a6dc8c17d543e93eb639c73661b05f6
Author: lijewski <mjlijewski@lbl.gov>
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 08a1d7974e1a655f736b0295701f35ae8f87f23f
Author: cmalone <malone@ucolick.org>
Date:   Tue Aug 30 15:04:33 2011 -0700

    get rid of all the *.mod files in the CWD
    
    Signed-off-by: lijewski <mjlijewski@lbl.gov>

Tools/C_mk/Make.Darwin

commit 74449ac63d05a1c5bfcc66d191bf48ac6dcb11a9
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 30 13:52:19 2011 -0700

    workd with USE_F90_MG=TRUE

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 3134b51ddd29a848aadfe986eb2be796906b0858
Author: lijewski <mjlijewski@lbl.gov>
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 87af60426e14f78d88e8f8e0623c142ed3f30bb8
Author: Ann Almgren <asalmgren@lbl.gov>
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 c042e7c56cc5e6b890dac68ce70f363a360b15c0
Author: lijewski <mjlijewski@lbl.gov>
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 765947bd0286e574d3c95d34cb664250ae8b565f
Merge: f4e754d df77494
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:12:38 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit f4e754d1f95ea74ba1cc7252672a711b42a0ec88
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:11:59 2011 -0700

    Chris' mod for macs

Tools/F_mk/GMakeMPI.mak

commit e905c1d4ecf7a85d543ff6ff4dafd9f735379dce
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Fri Aug 26 16:11:37 2011 -0700

    Chris' mod for mac's

Tools/C_mk/Make.Darwin

commit df774945f241d13b70ec953508541594611d04f8
Author: lijewski <mjlijewski@lbl.gov>
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 b92c343a694a2bfad207d1086dbdf762938ca882
Author: Theodore Kisner <tskisner.public@gmail.com>
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 <mjlijewski@lbl.gov>

Src/F_BaseLib/GPackage.mak

commit a9ab1ce1a92366736366fce1cc750a3a18435366
Author: Theodore Kisner <tskisner.public@gmail.com>
Date:   Thu Aug 25 15:15:03 2011 -0700

    Convert Cray vector merge functions to modern fortran merge syntax.
    
    Signed-off-by: lijewski <mjlijewski@lbl.gov>

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 50cadd0ec72a99ec0ba541965da0a6f3cce404c4
Author: lijewski <mjlijewski@lbl.gov>
Date:   Fri Aug 26 13:58:49 2011 -0700

    Removed some unused routines.

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f

commit 73d355db401ee91d2423b8d124a69128128a5527
Author: lijewski <mjlijewski@lbl.gov>
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 64dc0f1502e71714a348a55814738c998fea625a
Author: Ann Almgren <asalmgren@lbl.gov>
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 e807bbe683d15f27a856e97fb0eaab57c1f8f7da
Author: Ann Almgren <asalmgren@lbl.gov>
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/BoxLib.f90
Src/F_BaseLib/FParallelMG.mak
Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/box.f90
Src/F_BaseLib/box_f.f90
Src/F_BaseLib/boxarray.f90
Src/F_BaseLib/boxarray_f.f90
Src/F_BaseLib/boxlib_f.f90
Src/F_BaseLib/cluster.f90
Src/F_BaseLib/cluster_f.f90
Src/F_BaseLib/multifab.f90
Src/F_BaseLib/multifab_f.f90
Src/F_BaseLib/particles.f90
Src/F_BaseLib/particles_f.f90
Src/LinearSolvers/F_MG/FParallelMG.mak

commit caf3f9ebf19e2de5a1870f7532ddfa7c383169df
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 24 12:33:20 2011 -0700

    A simple commit to check that email notices are working.

Docs/GNUmakefile

commit 37b4b6d53044b074a3d66da6e7c2417677908e5c
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 23 14:04:30 2011 -0700

    Update the GNUmakefile in Tests/LinearSolvers/ComparisonTest

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 40232598e1319dda44652d831a338469697fc362
Author: vince <vebeckner@lbl.gov>
Date:   Tue Aug 23 14:00:08 2011 -0700

    email push test 0.  v.

Tests/C_BaseLib/tVisMF.cpp

commit de7c0e8d8b6f3180a5184e074e4a59d73ebee607
Author: lijewski <mjlijewski@lbl.gov>
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 093ff163bde1998b30cd10db1f7a087c291d74e0
Author: lijewski <mjlijewski@lbl.gov>
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 8949f1b4cf432f2d2ac49afe3466212f0ed8c2ea
Author: lijewski <mjlijewski@lbl.gov>
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 ae55f73d3a53feb12d0f1b9d55df47c2d9539aa3
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:14:08 2011 -0700

    Fixed comments to refer to new directory structure.

Src/F_BaseLib/FParallelMG.mak

commit 2a821bbf99b3132dc1e752d00910713a76120ce5
Author: Ann Almgren <asalmgren@lbl.gov>
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 8cef4c250a5d531bd21eacd25334c0664776213f
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:03:39 2011 -0700

    This now compiles.

Tests/LinearSolvers/C_TensorMG/GNUmakefile

commit 328f191a92ca01bf0080f788b381e5ccca0a69a4
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 13:01:56 2011 -0700

    Remove reference to iamrlib.

Tests/LinearSolvers/C_CellMG/GNUmakefile

commit d2c2c38d18201ea98550804c9f2e0445c8d454ee
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:59:09 2011 -0700

    No more reference to fboxlib.

Tests/LinearSolvers/C_CellMG/main.cpp

commit ca6b57132139aba36b7a925f5ec91e1b1d1f221f
Author: Ann Almgren <asalmgren@lbl.gov>
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 e2b0a645080550e0d81764a70ffad065e07681fc
Merge: e2456d1 35d9c40
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:38:39 2011 -0700

    Merge branch 'master' of almgren@gamera:/usr/local/gitroot/BoxLib

commit e2456d18349b729e74a2be13400cef507e1d599e
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:38:23 2011 -0700

    slight clean-up

Tests/LinearSolvers/ComparisonTest/main.cpp

commit 35d9c408794a22e947792c2dd8af048402e75dd2
Merge: 3cf0ba9 73ece67
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 17 12:37:05 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 73ece674b9afeafc8847727836170e2b419ec7f0
Author: Ann Almgren <asalmgren@lbl.gov>
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 f9b0b3dcf09973a7cadb21f22058becb704c95fb
Author: Ann Almgren <asalmgren@lbl.gov>
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 f2466e6ba5a3c11cf9db9880777b6911a8342da7
Author: Ann Almgren <asalmgren@lbl.gov>
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 367f14eb7ed804d4b26e00a8bd81a1b5716a5e18
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Wed Aug 17 12:12:03 2011 -0700

    Changes to try to get this to compile.

Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 3cf0ba963542df0eae03c6064d73ea4d8359d304
Author: Marc Day <MSDay@lbl.gov>
Date:   Wed Aug 17 11:00:33 2011 -0700

    Remove bibtex command

Docs/GNUmakefile

commit 92aa3d5100f4610172362a352d2b9e8d45dddddf
Author: lijewski <mjlijewski@lbl.gov>
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 9884a83ee14b9a1a7df495d5a5e26db3aface7ef
Author: lijewski <mjlijewski@lbl.gov>
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 a6089d48ab34d894d485d4b0fb7534bbadf917f3
Merge: c071cfc 47ee822
Author: lijewski <mjlijewski@lbl.gov>
Date:   Wed Aug 17 08:10:59 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit 47ee822fa1adb96d1e63279205c2c8967c540940
Author: Ann Almgren <asalmgren@lbl.gov>
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 51c03405a0bf4a75b89a569072897da840c4eb8e
Author: Ann Almgren <asalmgren@lbl.gov>
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 e393c7f125dc74719d27e735ac55a8e0e034351b
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 20:53:16 2011 -0700

    PBOXLIB_HOME --> BOXLIB_HOME

Tests/C_BaseLib/GNUmakefile

commit caae5456da98c941b79a6e138ee8e2d16afe6ad3
Author: Ann Almgren <asalmgren@lbl.gov>
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 c1bbaf67fa33de4cc8c6a3fe17c9da8ec455017f
Author: Ann Almgren <asalmgren@lbl.gov>
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 11ce5675a6cd6f7dd3a6d15915b14b28cf3ea306
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 18:18:00 2011 -0700

    Better for new BoxLib structure...

Tools/F_mk/GMakedefs.mak

commit c071cfcd2976cda7ce37af3ace85b0a8a7320d7b
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 16 16:34:11 2011 -0700

    No longer keeping around the POSIX Pthread stuff.

Src/C_BaseLib/Thread.H

commit 08b4e376a60c1a9f8e0f39dea5b2077a0941fc13
Merge: d9b487c 8942fb1
Author: lijewski <mjlijewski@lbl.gov>
Date:   Tue Aug 16 16:25:05 2011 -0700

    Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib

commit d9b487c60310ddd014c8b2cd8eb8069f7a251303
Author: lijewski <mjlijewski@lbl.gov>
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 8942fb1ee1cef682a5102c9454a1de6eb449f6a5
Author: ajnonaka <AJNonaka@lbl.gov>
Date:   Tue Aug 16 15:36:49 2011 -0700

    progress toward getting fParallel stuff to compile

Tools/F_mk/GMakedefs.mak

commit 2aab2f6a480b2089d5fb88b967b4576ba45f50f9
Author: Ann Almgren <asalmgren@lbl.gov>
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 33503d4f93c2a8bd0edf96c0e5240036ed3e48ef
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Tue Aug 16 14:11:51 2011 -0700

    Change FPARALLEL --> . or ..  (i.e. fix paths)

Tools/F_mk/GMakedefs.mak

commit 4c3b77b7c854e9ac59be3f6438e096506f8d5ba9
Author: mjlijewski@lbl.gov <lijewski@lijewski.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 8a264cd961a93c9210037864723dd1d9c35d0cf5
Author: mjlijewski@lbl.gov <lijewski@lijewski.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 51c69739edb8a98da79b5a52e8acdf4b0179de14
Author: Ann Almgren <asalmgren@lbl.gov>
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 8b979a3aafc2085dbe64cc9ebf9a0464d3795051
Author: Ann Almgren <asalmgren@lbl.gov>
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
Src/LinearSolvers/C_CellMG/Test/grids/grids.213
Src/LinearSolvers/C_CellMG/Test/grids/grids.25600
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
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_128cubed
Src/LinearSolvers/C_CellMG/Test/grids/in.3_256cubed
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_512cubed
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.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
Src/LinearSolvers/C_CellMG/Test/inputs.2d
Src/LinearSolvers/C_CellMG/Test/inputs.3d
Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp
Src/LinearSolvers/C_CellMG/Test/main.cpp
Src/LinearSolvers/C_CellMG/Test/vpramps.dat
Src/LinearSolvers/C_NodalMG/Test/files.2d
Src/LinearSolvers/C_NodalMG/Test/files.3d
Src/LinearSolvers/C_NodalMG/Test/gt_breaks_27pt
Src/LinearSolvers/C_NodalMG/Test/inputs
Src/LinearSolvers/C_NodalMG/Test/proj.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/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 e9f3f8c22958c6f4cceff1cc70fd4a242c2d1489
Author: Ann Almgren <asalmgren@lbl.gov>
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 8d3122395bd82ea9ccf56cbd988a457a8d4b6463
Author: Ann Almgren <asalmgren@lbl.gov>
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
Src/C_BaseLib/test/ba.15784
Src/C_BaseLib/test/ba.213
Src/C_BaseLib/test/ba.23925
Src/C_BaseLib/test/ba.25600
Src/C_BaseLib/test/ba.3865
Src/C_BaseLib/test/ba.5034
Src/C_BaseLib/test/ba.60
Src/C_BaseLib/test/ba.95860
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 f8ff102c9dbd9e8520f375c7d64d23396dac7596
Author: mjlijewski@lbl.gov <lijewski@lijewski.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.

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/BCRec.H
Src/C_AMRLib/Cluster.H
Src/C_AMRLib/Cluster.cpp
Src/C_AMRLib/Derive.H
Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/FluxRegister.H
Src/C_AMRLib/Interpolater.H
Src/C_AMRLib/LevelBld.H
Src/C_AMRLib/SlabStat.H
Src/C_AMRLib/StateData.H
Src/C_AMRLib/StateDescriptor.H
Src/C_AMRLib/StationData.cpp
Src/C_AMRLib/TagBox.H
Src/C_BaseLib/Arena.H
Src/C_BaseLib/Array.H
Src/C_BaseLib/BArena.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/BoxDomain.H
Src/C_BaseLib/BoxLib.cpp
Src/C_BaseLib/BoxList.H
Src/C_BaseLib/CArena.H
Src/C_BaseLib/CoordSys.H
Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/FArrayBox.H
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/IntVect.H
Src/C_BaseLib/Looping.H
Src/C_BaseLib/MultiFab.H
Src/C_BaseLib/Orientation.H
Src/C_BaseLib/PArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/Pointers.H
Src/C_BaseLib/REAL.H
Src/C_BaseLib/RealBox.H
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/Utility.H
Src/C_BaseLib/Utility.cpp
Src/C_BaseLib/VisMF.H
Src/C_BaseLib/docxx_squish.sty
Src/C_BoundaryLib/BndryData.H
Src/C_BoundaryLib/BndryRegister.H
Src/C_BoundaryLib/BoundCond.H
Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/InterpBndryData.H
Src/C_BoundaryLib/Mask.H
Src/LinearSolvers/C_CellMG/ABecLaplacian.H
Src/LinearSolvers/C_CellMG/CGSolver.H
Src/LinearSolvers/C_CellMG/GNUmakefile
Src/LinearSolvers/C_CellMG/Laplacian.H
Src/LinearSolvers/C_CellMG/LinOp.H
Src/LinearSolvers/C_CellMG/MultiGrid.H
Src/LinearSolvers/C_NodalMG/GNUmakefile
Src/LinearSolvers/C_TensorMG/DivVis.H
Src/LinearSolvers/C_TensorMG/MCCGSolver.H
Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H
Src/LinearSolvers/C_TensorMG/MCLinOp.H
Src/LinearSolvers/C_TensorMG/MCMultiGrid.H

commit 5670b5bf51594f0574064e222188042046edde89
Author: mjlijewski@lbl.gov <lijewski@lijewski.lbl.gov>
Date:   Mon Aug 15 12:11:54 2011 -0700

    Removed old CVS embedded version strings.

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 b64c6562ee8f7cc0e2a02409e8ba004219bde137
Author: mjlijewski@lbl.gov <lijewski@lijewski.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 a88c944ff43d29d9f020078586c9df6903ee9192
Author: mjlijewski@lbl.gov <lijewski@lijewski.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 2ea54a393b2f80e119624c7e479617e08d00a381
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:55:47 2011 -0700

    Remove all Banner.html

Src/C_AMRLib/Banner.html
Src/C_BaseLib/Banner.html
Src/C_BoundaryLib/Banner.html

commit c06f48f5d5993c67ea0d33af53d955bfe14fffac
Author: Ann Almgren <asalmgren@lbl.gov>
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 3386f7da1304a22ed7c258705c1be309849b86e4
Author: Ann Almgren <asalmgren@lbl.gov>
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 1723679da4edcb73ee8a89504861d6c990b5987b
Author: Ann Almgren <asalmgren@lbl.gov>
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 e9bd38eb0543d7bc810a8841d9d7c27fed611c75
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:45:28 2011 -0700

    Remove cvs tags.

Src/C_AMRLib/ARRAYLIM_1D.F
Src/C_AMRLib/ARRAYLIM_2D.F
Src/C_AMRLib/ARRAYLIM_3D.F
Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/AuxBoundaryData.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.cpp
Src/C_AMRLib/FILCC_1D.F
Src/C_AMRLib/FILCC_2D.F
Src/C_AMRLib/FILCC_3D.F
Src/C_AMRLib/FLUSH_F.H
Src/C_AMRLib/FLUXREG_1D.F
Src/C_AMRLib/FLUXREG_3D.F
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/Make.package
Src/C_AMRLib/PROB_AMR_F.H
Src/C_AMRLib/SLABSTAT_1D.F
Src/C_AMRLib/SLABSTAT_2D.F
Src/C_AMRLib/SLABSTAT_3D.F
Src/C_AMRLib/SLABSTAT_F.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

commit 0853d78c215cfc89ff19852e7e37688ba7531b24
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:39:15 2011 -0700

    Removing cvs tags.

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 7470963748594addac6aaed1a1c416e4e071d916
Author: Ann Almgren <asalmgren@lbl.gov>
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 1045ed9d8e72715cb29aa0aa0c53f7a94fb35be9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:26:58 2011 -0700

    Deleted Banner and  removed CVS Id's from other files.

Src/LinearSolvers/C_CellMG/Banner.html

commit be145dc54dc3491e4d194a7cfc437b81452e6521
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 15:18:45 2011 -0700

    Remove reference to FBOXLIB_HOME.

Src/LinearSolvers/C_to_F_MG/Make.package

commit 8946379ebf787c5d33faf5a826d1f7ca833baff9
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Sat Aug 13 14:51:36 2011 -0700

    Fix $(TOP) --> $(PBOXLIB_HOME) for Tools/...

Tools/C_mk/Make.rules

commit 32aef1e65e8f6e4301c2d41de6977cdd6dc043d0
Author: Ann Almgren <asalmgren@lbl.gov>
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 3bab94175177e141d5a2149eab8cc2574bd5e76d
Author: Ann Almgren <almgren@gamera.lbl.gov>
Date:   Fri Aug 12 19:32:57 2011 -0700

    changed script

Tools/C_mk/Make.rules

commit 39c83ae9990acfc20434902adc1fd2fee6410d04
Author: Ann Almgren <asalmgren@lbl.gov>
Date:   Fri Aug 12 19:28:33 2011 -0700

    changed script location

Tools/C_mk/Make.rules

commit 7b4725caff4607cbcfa8196c467a5c30ccd1b754
Author: Ann Almgren <almgren@gamera.lbl.gov>
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 774eac855d0a663b87bbc838421a63c7934adff7
Author: Ann Almgren <asalmgren@lbl.gov>
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 dbb2cf44a4e78b49d6b22a9ec7c9a4b03923279f
Author: almgren <almgren>
Date:   Thu Aug 11 13:47:16 2011 +0000

    This now includes the particles.

Src/C_AMRLib/Make.package

commit 7c645e6c22e78a7e1e5275d51fe50c7a822462ff
Author: almgren <almgren>
Date:   Wed Aug 10 22:11:31 2011 +0000

    Fix oops.

Src/C_BaseLib/Make.package

commit 5674ef7050fc42a42d414176ce7769dff7aba872
Author: ajnonaka <ajnonaka>
Date:   Wed Aug 10 20:33:52 2011 +0000

    added support for Intel12 on hopper

Tools/F_mk/comps/Linux_intel.mak

commit 363d9153cc5d5bf52f4916ec5505228cc1c664fb
Author: almgren <almgren>
Date:   Wed Aug 10 20:19:41 2011 +0000

    Remove RealBox, CoordSys and Geometry stuff.

Src/C_BoundaryLib/Make.package

commit 814bf8ac61f9b845ca53df281bce4a61d4fc4e2e
Author: almgren <almgren>
Date:   Wed Aug 10 20:18:57 2011 +0000

    Added RealBox, CoordSys, Geometry stuff.

Src/C_BaseLib/Make.package

commit 5545e5760409c9aa0aa0fb2f905ca780dee3f539
Author: almgren <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 16723e91d437860e201271fa28abc9e058f688e8
Author: almgren <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 da611c7af56b0a8896bf71cae7f116657418b3e8
Author: lijewski <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 6fdd4e5d4b61af386b54f95a3d513e72ed48e83b
Author: lijewski <lijewski>
Date:   Tue Aug 9 21:32:45 2011 +0000

    added clear() to DeriveList

Src/C_AMRLib/Derive.H

commit 0f091e4f9fd05c6fe06f4152b2240fb8594288f6
Author: lijewski <lijewski>
Date:   Tue Aug 9 16:36:54 2011 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit cda44e2ca8a6aa571f7549251774172ef25bdf42
Author: lijewski <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 8d7d258a0601c335ce4e501bfd559a62fc81ccb7
Author: lijewski <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 cd99a72952d76d217d23c423da18af0b8a569e17
Author: lijewski <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 06f9820e1d8f25042cebcb24444204a9bae24050
Author: lijewski <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 9fe43bac57ae0d3013384c6a23f797ea38628c50
Author: lijewski <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 5182942ce238ae1dec64b64b0a53529cffd4c90f
Author: lijewski <lijewski>
Date:   Mon Aug 8 20:37:25 2011 +0000

    more work on Initialize()/Finalize()

Src/C_AMRLib/Amr.cpp

commit 1262f30784175f8fe04766180381dea5ddbed8aa
Author: lijewski <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 6a873f0b16d64137869cdf1bc1586aa69a80f413
Author: lijewski <lijewski>
Date:   Mon Aug 8 16:58:44 2011 +0000

    add clear() to ErrorList

Src/C_AMRLib/ErrorList.H

commit e45e13fe10f8419199fb44c402f40d94bf0ad016
Author: lijewski <lijewski>
Date:   Sat Aug 6 02:57:14 2011 +0000

    turn on/off cache statistics with geometry.verbose

Src/C_BaseLib/Geometry.cpp

commit 98def4c308bd32a77af45914a1bd991590225e21
Author: lijewski <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 06a835e73f7ed81c0daa7445646218c19615bca4
Author: almgren <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 b93b8cfe11c2b3143adcb947643e7772a5018513
Author: lijewski <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 db783b7f28b6fbe76a3f93b8b07fc87514c060d1
Author: lijewski <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 d2ba695c2157a2aaefbb91f68708a8ba7bd651c1
Author: almgren <almgren>
Date:   Fri Aug 5 22:28:02 2011 +0000

    Needed ParmParse.H ...

Src/C_AMRLib/Particles.H

commit f378f62bca28e667d7e67c35425703ce1ea43dd6
Author: lijewski <lijewski>
Date:   Fri Aug 5 22:21:16 2011 +0000

    some cleanup

Src/C_BoundaryLib/InterpBndryData.cpp

commit 25da41aa71ae5908bdee5cc6f791808e30ef3859
Author: lijewski <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 215a39433faa50dfdaf3bc68e3a9047623eba742
Author: lijewski <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 18cb705fb09783c558e6ac373bb853ea74c9a109
Author: almgren <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 51adc18f2e20bf3888e915616396e06609f16503
Author: lijewski <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 a9cc80ae4f3b36828e151cfde51f1759d041d41d
Author: lijewski <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 df55e9fbd3585d0891c92d316bfbdb58e03c3b7d
Author: lijewski <lijewski>
Date:   Thu Aug 4 19:36:57 2011 +0000

    flush the CPC cache in Finalize()

Src/C_BaseLib/FabArray.cpp

commit 4335f7c5d72dc132e0248cfec7afb111e4fae190
Author: almgren <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 c95466b3881f13237a114d720042a67b7f5448ba
Author: lijewski <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 371422edd3b22cf37b7f7db3b9c23828cb88c927
Author: lijewski <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 f02e765810e2bc2d16742e6cefa0ba974e03fd57
Author: almgren <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 2a4fdb95436731421f83a01c8d4b091ec26723ea
Author: almgren <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 918bc1d4a64e8850da874c38312485012cf3cb2f
Author: lijewski <lijewski>
Date:   Wed Jul 27 19:48:05 2011 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile
Tests/LinearSolvers/ComparisonTest/GNUmakefile

commit 47f6e1a5468e1939e600b2dff95b43f1618509b1
Author: marc <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 36aae26414594f0d1978f21026e982223bafe4f7
Author: lijewski <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 6f4f22cf235daa6bea7b49d77604fb99ce55d451
Author: mzingale <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 59571563e768118c82f0996a4fd83a48ff942787
Author: lijewski <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 6cb9e3cd16a926bc65e3573787d3d9e6f7c7c1f5
Author: mzingale <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 b48ee7065218403570b3f8584e2c16f251f43274
Author: almgren <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 507808bc89f8cc0ef0ffe00bfc2bea1af7c9f70a
Author: almgren <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 4482386b0b1c33a8fef9c6cec591691b5ad67bb8
Author: almgren <almgren>
Date:   Wed Jul 20 14:37:52 2011 +0000

    Add BC_GEOM.

Src/LinearSolvers/F_MG/bc_functions.f90

commit 4730bbbe0e6c734ebbd591de6ef0ec7dca621ae7
Author: mzingale <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 0f548887d21ba25aa4af1e83a651e2ed664f9bc1
Author: almgren <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/mg_restriction.f90
Src/LinearSolvers/F_MG/ml_restriction.f90
Src/LinearSolvers/F_MG/nodal_restriction.f90

commit 65297acc1299e66e3eacb9eb73070758bb6b3782
Author: almgren <almgren>
Date:   Wed Jul 20 05:20:47 2011 +0000

    Add edge_restriction file.

Src/LinearSolvers/F_MG/edge_restriction.f90

commit 1e3da324127f598bf8aa4fa9dd138ba943413d0f
Author: almgren <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 34d88900a8d6439a2a9f1600d14f4b2a7dc516c6
Author: almgren <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 9ca94ef87b02ba0a9251d1f6b15a47d33d6d0bf8
Author: almgren <almgren>
Date:   Wed Jul 20 04:32:44 2011 +0000

    Move applyop stuff into separate file.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 19040b6951e3d47168cf307895469d3d55954a31
Author: almgren <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 9df016746afe64358f3734b9d76867d87249a44c
Author: almgren <almgren>
Date:   Wed Jul 20 04:06:00 2011 +0000

    Forgot multifab_module.

Src/LinearSolvers/F_MG/ml_norm.f90

commit 81adbb460e1eccb4d09d9fa51c41e12ccecf085f
Author: almgren <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 21c10ac23f16e1be7e67133636c2efa497c4feea
Author: almgren <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 ec2390c4e1eecc51a3e1273bc0607d6d2c3d07eb
Author: almgren <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 80058bed05e6f2accbdc3b36d105e367da044b7f
Author: almgren <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/ml_interface_stencil.f90
Src/LinearSolvers/F_MG/nodal_interface_stencil.f90

commit 1fb6070c2bb1366231526eed54410f461b97f583
Author: almgren <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 3d341cba69a59f5b209dbbe49ab2db22f36ac7aa
Author: almgren <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 36a1462fbe24410e18b04540cfb091927e99cb34
Author: almgren <almgren>
Date:   Wed Jul 20 01:42:44 2011 +0000

    Changed name.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit a69f976d31a04b0763742443d8cf08b99c726c60
Author: almgren <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 c1eb5723c800d27301e46f464eef59085cdb1cc5
Author: almgren <almgren>
Date:   Wed Jul 20 01:36:49 2011 +0000

    Fix nodal_newu...

Src/LinearSolvers/F_MG/GPackage.mak

commit 1753ffc34b166da6dbf83fd7e53f6464350b6cd2
Author: almgren <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 19e612d3c3d4303d0d47b9eb6eacec37b3fa86fc
Author: almgren <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 e8d079b25c5b51eeefae21c189a7bd5b28eb4e56
Author: almgren <almgren>
Date:   Wed Jul 20 01:29:44 2011 +0000

    stencil --> ...

Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit f1d0622175afc8c95f1202f83cfd4585506bcbfc
Author: almgren <almgren>
Date:   Wed Jul 20 01:29:18 2011 +0000

    stencil_module --> ...

Src/LinearSolvers/F_MG/mg_tower.f90

commit 5a7ae4eb96603b30a632658f17d8d3f1d43324c4
Author: almgren <almgren>
Date:   Wed Jul 20 01:28:43 2011 +0000

    stencil -->...

Src/LinearSolvers/F_MG/ml_util.f90

commit 556d3711389736629317787bfc1279e2d1b854af
Author: almgren <almgren>
Date:   Wed Jul 20 01:27:28 2011 +0000

    fix oops.

Src/LinearSolvers/F_MG/bc_functions.f90

commit 2208b4a405e3175f55279abcb6753303098b5f7a
Author: almgren <almgren>
Date:   Wed Jul 20 01:26:43 2011 +0000

    add bl_spacedim.

Src/LinearSolvers/F_MG/bc_functions.f90

commit 92d5b68fca546a6a8d0197963faf25fdbc54ad8d
Author: almgren <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 8fdfa1eba96556286eea356217ac4653f0ad980e
Author: almgren <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 fec4f78936511d14ad59c36ff16b4f45be6bb301
Author: almgren <almgren>
Date:   Wed Jul 20 01:11:02 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90

commit 27b7ef92a9dada0d501cab1bd769cdc39d287c0a
Author: almgren <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 2ad5c979f1ac746aabd9d8ebb248e2f9109ccb14
Author: almgren <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/impose_neumann_bcs.f90
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 d337c3a6f2907cdf6104a7dfaa38986acd6a72cb
Author: almgren <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/mg_cpp.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
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_fill.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90

commit bc66ffd2168a0be05df0400fdf8562c52ca3424a
Author: almgren <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 9b85f71813d366774497ffda52d07473353940be
Author: almgren <almgren>
Date:   Wed Jul 20 00:36:27 2011 +0000

    Forgot to fix module name.

Src/LinearSolvers/F_MG/cc_smoothers.f90

commit 50cb0e6ce064098629595dcf18d091af0e729f5f
Author: almgren <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 7e719cdede84b128d491a76711622ca369b9d2eb
Author: almgren <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/mg_smoother.f90
Src/LinearSolvers/F_MG/nodal_smoothers.f90

commit d99b33d5a5213eb20ff367b9afee89d62db0fd59
Author: almgren <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 e3047a371edb76ea781ba19842b28a779b7c62f8
Author: lijewski <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 ad54a1e611571480aee0e65054866a0722317d21
Author: almgren <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 c3b66a45c2df14219273f16a71a15fbe9e8d408e
Author: marc <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 c0ee0f0d7024949354f23c6e107c1c66a2cb9374
Author: almgren <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 0c3cec3bb85fd777d9333d9a40ca4a811de0174d
Author: almgren <almgren>
Date:   Mon Jul 18 23:45:01 2011 +0000

    Remove unused variables.

Src/LinearSolvers/F_MG/stencil.f90

commit 61b7c4524b0358eac0c09de67f29a3e40c65b02b
Author: lijewski <lijewski>
Date:   Mon Jul 18 20:51:17 2011 +0000

    substitute istringstream for deprecated istrstream

Src/C_AMRLib/Amr.cpp

commit 685b23ae3612d29e4ee14bfad64489b412ab9669
Author: lijewski <lijewski>
Date:   Mon Jul 18 19:52:05 2011 +0000

    substitute istringstream for deprecated istrstream

Src/C_BaseLib/VisMF.cpp

commit 3e1246abb615e01bcecd73f0d9be3b6c14e5dd49
Author: lijewski <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 f9faba62dca6845506ca028879b0033a8b992b28
Author: lijewski <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 6a46c0192080964df74c5f3ba2eda12358a4e1cd
Author: lijewski <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 53b796f19fffc43f820719cf6e6aace7f918220f
Author: almgren <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 ca453237c5b36fce71eac881eddbbd54f7e5b3ba
Author: almgren <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 140d275d9bac9576a357f6c448eb9a2d574f3389
Author: lijewski <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 091de5cbace1e356fd9e50ba509c8696700a605e
Author: gilet <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 5b7487a65ff75d2026fd9b78b05f00613dcf8347
Author: almgren <almgren>
Date:   Thu Jul 14 21:24:35 2011 +0000

    Move LO_UTIL.F to bndrylib.

Src/LinearSolvers/C_CellMG/Make.package

commit 9e18adff4ab4d24e3c3a7c8d4a37a45026396ab1
Author: almgren <almgren>
Date:   Thu Jul 14 21:24:11 2011 +0000

    Add LO_UTIL.F

Src/C_BoundaryLib/Make.package

commit a690a0e114be17aab84e68decc68edbc0c345763
Author: lijewski <lijewski>
Date:   Thu Jul 14 16:53:26 2011 +0000

    ByteSpread() now also prints out total particle count.

Src/C_AMRLib/Particles.H

commit 195279b900be55a2f4b9244cd573de67bc56691a
Author: lijewski <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 dcd41c87c1f69396eeebfb03555ec208f741a6dd
Author: mzingale <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 eb62c53b045cfde29172927f2c64613f55bd3f67
Author: almgren <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 b5551be643ee4106634f9cf9117e13588f264b20
Author: almgren <almgren>
Date:   Wed Jul 13 21:27:31 2011 +0000

    Move files from mglib to here.

Src/C_BoundaryLib/Make.package

commit 53e6494593ee75135ef4d6c5351ccf89fcfe6c25
Author: almgren <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 bd18f00341da3c6ce06d5a0fe797eb90f3c49978
Author: lijewski <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 c642b775550b8e89296acd3564d44a24b50a14e7
Author: gpau <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 13a250e4eb77a48b0bd6baa3ac33ff43f9c3ef2b
Author: lijewski <lijewski>
Date:   Tue Jul 12 18:02:55 2011 +0000

    use memory a bit more efficiently in Redistribute()

Src/C_AMRLib/Particles.H

commit c86fa4695ac837582bdf9f5574aacf565e02ca82
Author: lijewski <lijewski>
Date:   Tue Jul 12 16:54:30 2011 +0000

    beefed up OK() a bit more

Src/C_AMRLib/Particles.H

commit 8e53caed16247af61d90fbe1c3bf2c14d286ce51
Author: lijewski <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 947fb706c2b6d8955a6037921cb844cacd153f12
Author: lijewski <lijewski>
Date:   Fri Jul 8 21:34:26 2011 +0000

    modest speedups and simplifications to estTimestep()

Src/C_AMRLib/Particles.H

commit 6967b7c379fa4f82a827d1ddfaec946f2a9ffe7e
Author: lijewski <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 8d3180a67ca30eca533c099d235e2e89a31f1ca3
Author: lijewski <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 b1ab379beadc08949857ac3e0a84bd517af4a8e4
Author: lijewski <lijewski>
Date:   Fri Jul 8 17:15:56 2011 +0000

    quiet some compiler warnings

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 5dbf4118285883df575ff1cb9e682551ba9fdb1d
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:42:38 2011 +0000

    quiet some compiler warnings

Src/C_BaseLib/Looping.H

commit 983bc0f0763dd1fb8e0a5507d75da4f2693a0fea
Author: lijewski <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 ceb3f24a1a829cb2f179bb0fd83c171cd9554fbc
Author: lijewski <lijewski>
Date:   Fri Jul 8 16:03:40 2011 +0000

    removed some unused variables

Src/C_BaseLib/BaseFab.H

commit 00a22d5ede723cb57de43480773162a1452a3972
Author: lijewski <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 bba19e122adcc51b93b0065200ac4929e87c2097
Author: mzingale <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 391d413b7db96d72fa1c47ecabc11ac1ac2ec004
Author: marc <marc>
Date:   Wed Jul 6 23:19:58 2011 +0000

    Add + and - to allowed characters in identifiers

Src/C_BaseLib/ParmParse.cpp

commit ae532cbea1d182642f1ed72747f1ed9c467b0d29
Author: almgren <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 522b1bf8c50a2c0650272d1b13c3aa3ab784f0ce
Author: lijewski <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 586f7b6ca002883fa6433e638fee7ac76f636593
Author: almgren <almgren>
Date:   Wed Jul 6 21:31:14 2011 +0000

    Fix periodic wraparound in multilevel AssignDensity.

Src/C_AMRLib/Particles.H

commit 88e7662bdffc6f364abebdf9ae3a210311bf57b9
Author: almgren <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 7d7f5cbee5c8c29480d252d03101f5752dca889b
Author: almgren <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 22838cfcc8270dbf64b2880754c92f681c4953ee
Author: almgren <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 1354ed707c676d73c84f12074aef5038f506aac4
Author: almgren <almgren>
Date:   Wed Jul 6 02:58:57 2011 +0000

    Add new routine -- MultiplyParticleMass -- used in SantaBarbara initialization.

Src/C_AMRLib/Particles.H

commit 25df466454bd540ea7f092ef8a3f20526b4ff0df
Author: almgren <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 2c06cb640c8d5453db8936ada92b10393c7b38bb
Author: almgren <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 ec0e20457e242a13276d959ceb3944ee67f95abc
Author: almgren <almgren>
Date:   Mon Jul 4 18:48:19 2011 +0000

    Fix initialization of multilevel Santa Barbara problem

Src/C_AMRLib/Particles.H

commit 7e7fe14f0c165c8f1cbfa76175c349487f71a29c
Author: gpau <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 da729fdb693dd8f22d439321135ae1ad949c382f
Author: gpau <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 9dc3d17b7eba49573d8e70da3a33aa6e5af05c43
Author: marc <marc>
Date:   Fri Jul 1 23:10:54 2011 +0000

    to facilitate derivation, if necessary

Src/C_BaseLib/ParmParse.H

commit 6fd6b0712b6e1cd865e0df952b6227b7dcd8370d
Author: marc <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 009eb0af4410952e00ab3acfa080f9b22e936d73
Author: almgren <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 5ad33e6c7ba99b91d028721b91055b46bc8a349c
Author: almgren <almgren>
Date:   Fri Jul 1 06:06:03 2011 +0000

    Don't print all the particles in InitFromAscii.

Src/C_AMRLib/Particles.H

commit 023cb64f8d417e25788a568c1078b198b777b22f
Author: almgren <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 9be548bb4d7282bc794b5892e4a3bd927e53705f
Author: almgren <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 832f075efd6467c5512e241b191b89b740ce1e72
Author: lijewski <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 d1f8921e333351b68b32f255bba16d3959ce4b1f
Author: lijewski <lijewski>
Date:   Wed Jun 29 15:10:42 2011 +0000

    got rid of some unused variables in Timestamp()

Src/C_AMRLib/Particles.H

commit bda6db560ad4a0c39913fadcd2ee8b545ff2d4a2
Author: mzingale <mzingale>
Date:   Wed Jun 29 13:31:30 2011 +0000

    store .mod files in o/ on nan

Tools/C_mk/Make.Linux

commit 294eadbd90c692080c4c317f35269db5768109dd
Author: mzingale <mzingale>
Date:   Wed Jun 29 13:12:13 2011 +0000

    switch to latest MPI for nan

Tools/C_mk/Make.mpi

commit 7b95af193539583622c41532042aa106546b10c4
Author: lijewski <lijewski>
Date:   Wed Jun 29 05:23:51 2011 +0000

    remove some debugging I/O

Src/C_AMRLib/TagBox.cpp

commit e7d78bb0a9a7c1bb7fcc7547659bdc4c8e4f16a4
Author: lijewski <lijewski>
Date:   Wed Jun 29 05:21:17 2011 +0000

    fix to previous mod when USE_MPI=FALSE

Src/C_AMRLib/TagBox.cpp

commit 6138342c2c7821cd8f33cc89aa214cbb5c9f7ff7
Author: lijewski <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 c865ef2ec22796fb676ee12d03cdc04c3cfebbb5
Author: mzingale <mzingale>
Date:   Tue Jun 28 21:51:33 2011 +0000

    no -module flag for nan

Tools/C_mk/Make.Linux

commit 16aecd6dc69f4477c30047509f29626423ce5662
Author: mzingale <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 01ca6e3e67f39e4eaf66df68139b261b877f24f3
Author: almgren <almgren>
Date:   Tue Jun 28 19:09:34 2011 +0000

    Remove characters from word.

Src/F_BaseLib/tag_boxes.f90

commit aa9445e4cbd258f6acebf33432365299d83ac41d
Author: marc <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 6aab3239d31273a7665637c2e05a72e7001c1a8e
Author: marc <marc>
Date:   Fri Jun 24 22:59:07 2011 +0000

    add hg file to list

Src/C_BoundaryLib/.cvsignore

commit 2815573c274a7a23225abd98462e6898c5fd37db
Author: marc <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 6b151be00d98f6a8a5adb338ac71bcf1fa9e5680
Author: lijewski <lijewski>
Date:   Fri Jun 24 21:03:23 2011 +0000

    more OMPing

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 5db3de4f63e56974efc9ee90481fe31e4b8a21f4
Author: lijewski <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 7e81f612a845fe9c7b8581dddf3351d2e13f050f
Author: lijewski <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 adfe9a5c3fba81944e84d123a810bf019cd33bc3
Author: lijewski <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 486514ce6d1d91e71630486ffc6c1170ef65cb41
Author: lijewski <lijewski>
Date:   Thu Jun 23 23:42:44 2011 +0000

    little more OMPing

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit ed54327e6d0ecd0b1a50b7be90b5a0b3627d603a
Author: lijewski <lijewski>
Date:   Thu Jun 23 20:10:33 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 1b969ad882e799db0ba660f146bebc7cc0c4aef6
Author: lijewski <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 7cdf73b872c7a7756b09c606ec74ee6dd1913cc0
Author: lijewski <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 14f5f41fe96df69697ae3d85e0dfd79cb74d696a
Author: lijewski <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 0f68a8e274847fba2a47e3865195d9da0384ff20
Author: lijewski <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 6dd119b948d6ede093f11d006c6032881c19952f
Author: almgren <almgren>
Date:   Wed Jun 22 01:27:02 2011 +0000

    max --> std::max

Src/C_AMRLib/Particles.H

commit 3d6742502d029487f8a05e2de72f54c064f70152
Author: almgren <almgren>
Date:   Wed Jun 22 01:24:55 2011 +0000

    Fix typo.

Src/C_AMRLib/Particles.H

commit cf29429bd23db382febfaf64a943e5b472423ae1
Author: almgren <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 13eeccd14962d0cf9c37e8ed0877b1b17b3a0f32
Author: almgren <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 edd57d610f3b2afc19d4a0a2a3733237be55ef07
Author: lijewski <lijewski>
Date:   Wed Jun 22 00:01:51 2011 +0000

    use O2 when optimizing

Tools/F_mk/comps/gfortran.mak

commit 1f946cb9e799adbd645a7482ea87e60245565ee4
Author: gilet <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 4e63435d3861384b29fa62a01621324cd20c4436
Author: lijewski <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 c6250667a9894072bd57a0ba3fc7bf0b804e4394
Author: lijewski <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 d71bb0ce659081e86102bbe48b177f2f79bb8b38
Author: celdred <celdred>
Date:   Tue Jun 21 18:25:32 2011 +0000

    added gojira entry

Tools/F_mk/GMakeMPI.mak

commit 11cdd46a1aa18c76f4b82ba15f5a703aea88f992
Author: lijewski <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 fd9dd5fb9dc16b56a45c75609e9adb2e5d6b8e80
Author: lijewski <lijewski>
Date:   Thu Jun 16 15:51:30 2011 +0000

    removed some XT3 junk

Src/C_BaseLib/Utility.cpp

commit f78280aced463907b7b46e21bf70067366baeb62
Author: lijewski <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 9291908019b7aba1599c48e2d626085289c6fd24
Author: lijewski <lijewski>
Date:   Tue Jun 14 20:35:35 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_2D.F

commit b677cf7587a15ced834bf165da452992bc577c70
Author: ajnonaka <ajnonaka>
Date:   Tue Jun 14 16:44:03 2011 +0000

    now printing lo/hi/avg FAB byte spread

Src/F_BaseLib/fab.f90

commit 74364aabaa73068b2b50e0ae6d6d732c95cfece7
Author: almgren <almgren>
Date:   Mon Jun 13 20:20:35 2011 +0000

    Need more files than we thought.

Src/LinearSolvers/C_CellMG/Make_nyx.package

commit c565ecfc4760a5857bb6503fbcd01629cf50d160
Author: almgren <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 b5da222c60158862ede94203fdb97b0fbb1a7a59
Author: lijewski <lijewski>
Date:   Fri Jun 10 23:48:03 2011 +0000

    quiet some unsed variable warnings

Src/C_AMRLib/Particles.H

commit baec2180b9dddc6fcc1092c0fb372ddc88c4e6a6
Author: lijewski <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 dea4af6351150aae43f1d51484f8ac8903b37667
Author: lijewski <lijewski>
Date:   Fri Jun 10 23:39:54 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_2D.F

commit 6d4f807926cfa4174c705f99a816666bac623e14
Author: lijewski <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 299689332e319dcd6799916d75a27d328318801a
Author: wqzhang <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 8a8203e98e3a3adcdd4a64617ec76c33a52bef46
Author: lijewski <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 07853c1cf9a5d074a30ef790ce54855573bb7827
Author: lijewski <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 fc7a2c2e658c1805561089a1731d97027c64aa93
Author: lijewski <lijewski>
Date:   Wed Jun 8 19:50:12 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit b708b6397377646257a3c023af59c9055d8b8949
Author: mzingale <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 bf08fe9b9de2000311598d8680bcd8888c8813cd
Author: lijewski <lijewski>
Date:   Tue Jun 7 21:53:57 2011 +0000

    just a little tidying up of things ...

Src/C_AMRLib/Particles.H

commit 0d285ff4c0dbe865941ac30ccec40b4e2f74bc6a
Author: gilet <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 815845f7bb4f3f847dfbf9906f07e77d0f544ed0
Author: lijewski <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 82a2510e323ec62868535a1587f627c8e72663b2
Author: almgren <almgren>
Date:   Mon Jun 6 22:15:21 2011 +0000

    oops.

Src/F_BaseLib/interp.f90

commit a28690dca4260c488fec8451d8a203079553960a
Author: almgren <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 f53119a5e3707b9000c73ecb52a1af38c9a16455
Author: lijewski <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 857a7129fe46af8de66fc1b6171da0d939a07249
Author: lijewski <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 85587e65aa23b18ad932427ed3d66ab36d4e4a4b
Author: almgren <almgren>
Date:   Mon Jun 6 18:52:27 2011 +0000

    Add fourth_order_interp_coeffs.f90

Src/F_BaseLib/GPackage.mak

commit 704ff0c459838089e58f442db1e5e52f289d290c
Author: almgren <almgren>
Date:   Mon Jun 6 18:51:45 2011 +0000

    Change name of module

Src/F_BaseLib/fourth_order_interp_coeffs.f90

commit b11143a955079ac5471ce8874dc26f08d198d77b
Author: almgren <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 4db70bc3f40069263ed396b5948482bda8155c37
Author: almgren <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 78ac29b1fd19decc496b29ce5d4300cdda26eafb
Author: lijewski <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 f2351a2f268d524a61491fb00832ac4250b56e2c
Author: ajnonaka <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 92cfd9e553a91f08bd5c192fe52d35a7f97e1098
Author: ajnonaka <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 8f3e8d4fd7fb113c5a48d06bd7db4740e63f119f
Author: mzingale <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 06f1e14cc2794547afdade862619a923e3c54f51
Author: lijewski <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 ac79d9c8dacb3d86884803b65ed346d2a2119a19
Author: lijewski <lijewski>
Date:   Thu May 26 21:11:27 2011 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit f2ff9233380c7bedff8f678b94d4922ede4a26f4
Author: lijewski <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 7e77e659fe84654e42c6509a6917a62b5a0276b9
Author: lijewski <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 776e4b688568cec5148d53d8a7da5f7fe92daf7c
Author: lijewski <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 e5fedf82f39e37f4aba0a7d3af6117f042d0105a
Author: lijewski <lijewski>
Date:   Thu May 26 17:01:35 2011 +0000

    initial cut at multifab_sum_boundary()

Src/F_BaseLib/multifab.f90

commit f8e2818beac2c3696cb951d1e6e221f0eb5946b6
Author: lijewski <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 64f354db9bd27f1519876dc47a9d171c123a947a
Author: almgren <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 baf0969bdffa78429469799481010cf23a9e7501
Author: almgren <almgren>
Date:   Mon May 23 20:52:14 2011 +0000

    Fix error message.

Src/F_BaseLib/particles.f90

commit db784ca3967dde67177ad3c3b9f94289a8cdb432
Author: lijewski <lijewski>
Date:   Mon May 23 20:30:21 2011 +0000

    added Tokenize()

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit f0e5a7262f1985332897c5fd1e3994b7b9075b1e
Author: almgren <almgren>
Date:   Mon May 23 18:42:30 2011 +0000

    Add comment.

Src/F_BaseLib/particles.f90

commit 83b9a8ca54af6185f5bb45c7648f16f4b86b06cf
Author: almgren <almgren>
Date:   Thu May 19 19:47:51 2011 +0000

    Added some debugging to InitCosmo.

Src/C_AMRLib/Particles.H

commit 05fc949f4be1061453164d76ca63d78f1aea509c
Author: almgren <almgren>
Date:   Thu May 19 18:21:52 2011 +0000

    New version of InitCosmo().

Src/C_AMRLib/Particles.H

commit ac4a76c37a96ee91a5d97d66b3754ee6581d1fc5
Author: lijewski <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 9de2aeba25aa82479f6a0296a7ef831bf2d2541b
Author: almgren <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 6ee09ccef5acf10e09ff3089a72f6cd85a6bd85c
Author: lijewski <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 bf573df91f390d32dac33f51de47b6d0d2047df7
Author: lijewski <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 6ced58a03ae655f315fb156e4431754b9969499c
Author: lijewski <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 b550f28bfec6cbe649d60cfcc4a771b82e7f5cd8
Author: lijewski <lijewski>
Date:   Mon May 16 21:48:02 2011 +0000

    fixed my typo

Src/C_AMRLib/Particles.H

commit d5d55215e957a53d7fd7e2a93943049f97a37d74
Author: almgren <almgren>
Date:   Mon May 16 21:13:58 2011 +0000

    Remove unused "grid"

Src/C_AMRLib/Particles.H

commit 3d9d0fdfad0d5b7837677e92b18ada3b5fc56523
Author: lijewski <lijewski>
Date:   Mon May 16 17:25:21 2011 +0000

    removed unused variable

Src/C_AMRLib/Particles.H

commit d8b7b689bb9e8cc0e928f39b7c8cbc68da905921
Author: lijewski <lijewski>
Date:   Sun May 15 18:29:36 2011 +0000

    added assert that DeriveFunc != 0 in derive()

Src/C_AMRLib/AmrLevel.cpp

commit d0870c58233ce2c55008deb46b8000d49196bc6c
Author: lijewski <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 674cb1867b66a22d98709ea291296ee31b960dbd
Author: lijewski <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 7df89127329fe9654fce6ef2f48d224aca3b1fe3
Author: almgren <almgren>
Date:   Fri May 13 21:54:27 2011 +0000

    Make the two Increment routines have separate names.

Src/C_AMRLib/Particles.H

commit b73ad2680871a65885dc3b50b0cb72f9d2750798
Author: almgren <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 982d13f5d20af40181017a2dcbffc41237dc2cfb
Author: almgren <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 993a50ece9a698ea1d59ced039e47921a3a65e49
Author: almgren <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 f257079eb376224f4cd8d564126f507c51c4d9cd
Author: almgren <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 8b96bf627f19ac40a90c3823f9b8435d30b50563
Author: lijewski <lijewski>
Date:   Thu May 12 22:20:33 2011 +0000

    removed names from Timestamp

Src/C_AMRLib/Particles.H

commit bac09666619461957d350cfe0f2d9f82fd45360d
Author: lijewski <lijewski>
Date:   Thu May 12 20:58:44 2011 +0000

    close() Timestamp file after flush()

Src/C_AMRLib/Particles.H

commit b464cf223e59b0fe2953c6da4430c0db95aa0d15
Author: lijewski <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 8bc648e3df6c18aa746bd727e524bc72e81db0a3
Author: lijewski <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 60c408f21723411568f8c111e80455e1e792e94b
Author: lijewski <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 2bab199c83876a4f26c0fe090e5d4ae0f350c249
Author: lijewski <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 cdf1d28eb7f3cef4d29a3c8899a225efd1cb095c
Author: lijewski <lijewski>
Date:   Tue May 10 04:55:21 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.H

commit 11496dbf99136717cf8d5cf6b6dbb1090238538d
Author: lijewski <lijewski>
Date:   Mon May 9 20:03:29 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit 4ecef25f64d4b2d08c1ca0d2e784e0ef3c788dbe
Author: lijewski <lijewski>
Date:   Mon May 9 19:48:36 2011 +0000

    just use MyProc when setting initial m_cpu

Src/C_AMRLib/Particles.H

commit a6e3de95f52692fb1abe0f2dc02455b182f40e1e
Author: lijewski <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 a7b2b08a76ceff86fe04b242cae3e458972b3251
Author: lijewski <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 005328d7cff938296d72e97ec29b9ed8a207f93c
Author: lijewski <lijewski>
Date:   Mon May 9 05:51:58 2011 +0000

    some I/O mods

Src/C_AMRLib/Particles.H

commit c66fd71313ac93f59e3e022ff20423bf9f0e686f
Author: lijewski <lijewski>
Date:   Mon May 9 05:51:03 2011 +0000

    removed some I/O

Src/C_AMRLib/Particles.cpp

commit 6d3e4367263341da38b978551a64a77e1cff3047
Author: lijewski <lijewski>
Date:   Mon May 9 04:35:50 2011 +0000

    print count of particles removed in RemoveParticlesNotAtFinestLevel()

Src/C_AMRLib/Particles.H

commit ecb5e2c80081124cb9ea68ddba803a3497bc31aa
Author: lijewski <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 b0157b7c4344a7d9944a3674b5558249e59351dc
Author: lijewski <lijewski>
Date:   Mon May 9 01:25:38 2011 +0000

    fixed some debug output when DIM=2

Src/C_AMRLib/Particles.H

commit 2a1c671b43122a393063b75ad5e95236584112d5
Author: lijewski <lijewski>
Date:   Mon May 9 00:09:20 2011 +0000

    refinement to Timestamp()

Src/C_AMRLib/Particles.H

commit 90c2093d82551068d67d5348d8b99832cca73770
Author: lijewski <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 a68a43c985e9340e7aafc954608048639697ae02
Author: lijewski <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 e6d4706e9297c294f364e87beb63a992431431c1
Author: lijewski <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 cfc3e121f6c54dfc5f9f384187138ae93a4569ec
Author: lijewski <lijewski>
Date:   Sat May 7 00:16:22 2011 +0000

    InitFromAsciiFile() is now much faster in parallel

Src/C_AMRLib/Particles.H

commit 6a685382d84e5693200086dc31b776ceca9109c1
Author: lijewski <lijewski>
Date:   Fri May 6 21:52:07 2011 +0000

    changed AdvectWithUmac() to John's satisfaction

Src/C_AMRLib/Particles.H

commit a75884e390c97f0ef40b138d181efc3b780d6fec
Author: lijewski <lijewski>
Date:   Fri May 6 21:21:07 2011 +0000

    modest speedup to InitFromAsciiFile(); more to come ...

Src/C_AMRLib/Particles.H

commit e9e7470fed2272736cc9c74380ba3a425f0b7f9c
Author: almgren <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 cb6e3d98c2d95fb42c73e46a89b89546c91dadd7
Author: almgren <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 e44d65857cdf0b5a6525c7fcb68d2a6dd6b39b66
Author: lijewski <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 6d03b16bd05fd88bf7271a9e54c5612e481082b2
Author: lijewski <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 e88dddf01cadbf788152057c90140af1c77f83fc
Author: lijewski <lijewski>
Date:   Wed May 4 19:46:04 2011 +0000

    early exit from Increment()

Src/C_AMRLib/Particles.H

commit 605884642822b536f131d7e843ecd0aa3223b8c6
Author: lijewski <lijewski>
Date:   Wed May 4 17:10:37 2011 +0000

    added RemoveParticlesNotAtFinestLevel() needed by HeatTransfer

Src/C_AMRLib/Particles.H

commit 693f459f4d079dcd967bb6f95dd1bc688465d55a
Author: lijewski <lijewski>
Date:   Tue May 3 21:01:37 2011 +0000

    removed some excess whitespace when printing in verbose

Src/C_AMRLib/Particles.H

commit 82e41c43b9c2ef8ae5ae975443ea370c89013b3c
Author: lijewski <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 02695422061820d45873bc32039f617256c94c6c
Author: lijewski <lijewski>
Date:   Tue May 3 19:21:09 2011 +0000

    refinement to how we reset NextID()

Src/C_AMRLib/Particles.H

commit 2aedc5f53e0744d7e13bcf8ea7b3ef617a8f3e63
Author: almgren <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 fbe7c65160c6ba748d9d760d99db5c5c0f993484
Author: almgren <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 d4a00477d5787991764f81c053780e2fa437714d
Author: lijewski <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 450486d8e81c8612d29fe7d73588e9f61ad4494f
Author: almgren <almgren>
Date:   Thu Apr 28 21:59:53 2011 +0000

    Correct criterion for destroying gcrse.

Src/F_BaseLib/fillpatch.f90

commit e9d8f693f9d1d7e360910b00a2548e5b72a3287e
Author: almgren <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 28650c3c29d14ce24d9cdfdbd6a269a0ded7fbc8
Author: almgren <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 0f7222451b2ef7c3674389623b76f0bb4a8ffa4a
Author: almgren <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 9d9d75484b1c8f8a0cbdc5fa43c1c80588cb2d15
Author: almgren <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 09cb63fe4a26628c69f2b40c26f121c0d2555424
Author: almgren <almgren>
Date:   Sun Apr 24 21:08:15 2011 +0000

    Add stubs for fourth order interpolation routines.

Src/F_BaseLib/interp.f90

commit 9f4b11dd03f45843e13d8338b1387292483a1cc9
Author: lijewski <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 ff7c1dc677d145b3031d85a7f72f22e0dd32b584
Author: lijewski <lijewski>
Date:   Fri Apr 22 21:37:17 2011 +0000

    changed some 0 -> ZERO

Src/LinearSolvers/F_MG/stencil.f90

commit 2adea4dba94b682c675f8417f3b80d147b5f0c55
Author: almgren <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 4a8196886bf909425d84d1e2a7f96ccb375e3b63
Author: almgren <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 b0aa3d5d85f7c77112d8fbb46b178b7ff02c574b
Author: almgren <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 a52813126f4ecb792a0ebafa76e10a77fc894aba
Author: almgren <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 6ad77c451b572c5a0916b660410bd41dec7f421e
Author: almgren <almgren>
Date:   Fri Apr 22 18:49:40 2011 +0000

    Adding additional print statement.

Src/LinearSolvers/F_MG/ml_cc.f90

commit f5a3eeae6f3fd0d18c953503f4c9cdcf1d2290c4
Author: ajnonaka <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 63ce685d1a068b2b704b1e032323be15dccad20a
Author: lijewski <lijewski>
Date:   Wed Apr 20 20:08:44 2011 +0000

    use CC wrapper instead of crayc++ for Cray

Tools/C_mk/Make.Linux

commit 908dc5e860846498385e06f296d1d5c7642492ee
Author: lijewski <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 39ae8b3c87737dc1e87c7973f883f312b1c3c153
Author: marc <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 2635c9c6d1473d2fb860ef64091caad1c94fa10d
Author: lijewski <lijewski>
Date:   Wed Apr 13 21:15:20 2011 +0000

    some OMP

Src/C_AMRLib/FLUXREG_3D.F

commit a97fe5d304dba7becaf09145fc4cba82dceaed0f
Author: lijewski <lijewski>
Date:   Wed Apr 13 21:03:26 2011 +0000

    minor performance improvement

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 55eb06b7dc53fbcb3d9e091e88c9a2b438a6c24f
Author: almgren <almgren>
Date:   Fri Apr 8 18:46:32 2011 +0000

    Get rid of extra characters.

Src/F_BaseLib/make_new_grids.f90

commit cd0e19f8a0da727a603b578faea63a5ec424c8e0
Author: marc <marc>
Date:   Fri Apr 8 01:34:01 2011 +0000

    *** empty log message ***

Tools/C_util/ViewMF/viewMFcol.cpp

commit f5f4666586a88cc56957fcd518011c69336505e1
Author: lijewski <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 f12fbc91d63c458b990fdbbff06c025f874eda04
Author: lijewski <lijewski>
Date:   Sat Apr 2 23:26:07 2011 +0000

    minor simplification of AssignDensity()

Src/C_AMRLib/Particles.H

commit 82ab1bb973d33b8cb3ce36d007589084d6c2aa8f
Author: lijewski <lijewski>
Date:   Fri Apr 1 23:15:23 2011 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit f457f3aecf5f59bf196d84646b1ec060e8c634d1
Author: lijewski <lijewski>
Date:   Fri Apr 1 17:36:21 2011 +0000

    added GPROF stuff

Tools/F_mk/comps/gfortran.mak

commit 89933d91bd53141c6933fca0489ad05681415747
Author: almgren <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 e861d88b762ecb67f4cec33291376ac9198dba81
Author: lijewski <lijewski>
Date:   Thu Mar 31 16:59:12 2011 +0000

    added a little commented out debugging code

Src/C_BaseLib/Geometry.cpp

commit 73a594e109c38c55413b45a6433eb97f4ddeff9d
Author: lijewski <lijewski>
Date:   Thu Mar 31 16:17:04 2011 +0000

    got to call new SumPeriodicBoundary() with correct Geom

Src/C_AMRLib/Particles.H

commit 3e76426b6d945d83e3187a4c876ed97ff6c7ea3e
Author: lijewski <lijewski>
Date:   Wed Mar 30 23:59:27 2011 +0000

    integrated in new SumPeriodicBoundary(dstmf,srcmf)

Src/C_AMRLib/Particles.H

commit eefb2ed9f75c078b31f106fc8442c7a14bfcd066
Author: lijewski <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 164218bfd121a1fcc83a701d98b98dd301e0215d
Author: lijewski <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 86b7ff10c1f6690ed1038ce96100088f00a510b9
Author: almgren <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 fa2704113bfdcdabdfa927ee71e3e69305ffd387
Author: almgren <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 42740248cc895aea2657556a44f310fdb87432c2
Author: lijewski <lijewski>
Date:   Wed Mar 30 18:16:59 2011 +0000

    modest improvement to bndry_reg_copy()

Src/F_BaseLib/bndry_reg.f90

commit e8b5492106ccb62f5609e4d77c73551a2f7905c4
Author: almgren <almgren>
Date:   Wed Mar 30 17:44:22 2011 +0000

    Add setval of tcmf.

Src/C_AMRLib/Particles.H

commit 639adad40603a008ed1e6a7eb85e36df63567751
Author: almgren <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 1449b4475e85b435c1e55708a7339070ac31e17d
Author: lijewski <lijewski>
Date:   Tue Mar 29 20:48:25 2011 +0000

    yet more work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H

commit 86bedf1f31b4b61fe2836364bf0a2a28256685c5
Author: lijewski <lijewski>
Date:   Tue Mar 29 20:35:46 2011 +0000

    more work on multi-level AssignDensity()

Src/C_AMRLib/Particles.H

commit 2e607c6ec3c47588f94d9efc76ca681fd73a9900
Author: lijewski <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 1ff8b6c60beea137c5bc0c00dec796c32a2711b5
Author: lijewski <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 efa64dda0100f8c22a6937a18b76089f95944f3c
Author: lijewski <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 df8f39e69bf64e688be67dbf6fac14113a4443ac
Author: lijewski <lijewski>
Date:   Mon Mar 28 23:00:26 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles_3D.F

commit 546dc04d610a66ffa2ade5411840500312715619
Author: lijewski <lijewski>
Date:   Mon Mar 28 23:00:13 2011 +0000

    added AssignDensityDoIt()

Src/C_AMRLib/Particles.H

commit 33521bafebe5b344063677ca39b2028d63365af3
Author: lijewski <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 daf83bee7ed0c0fe46ddc72600d3469b0cef00cf
Author: lijewski <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 deeef1897a44aba4a4faa4e53755439cae10d5e1
Author: lijewski <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 51ba655bac551c1aa9ed204644295def2755f583
Author: lijewski <lijewski>
Date:   Mon Mar 28 16:19:35 2011 +0000

    mod to quiet g++

Src/C_AMRLib/Particles.H

commit 146912ef7a3289d09b79be4154cc0dcf7df1ee3a
Author: lijewski <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 afc37515da2d136cf9c2c40ab4a442e9b5dae86b
Author: lijewski <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 bed95c1771e0162447b847c7e30b3ea48bda9700
Author: lijewski <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 9044bb515ab7073fbd6ce16a13426c00d1bc300b
Author: lijewski <lijewski>
Date:   Thu Mar 24 20:50:43 2011 +0000

    some OMP refinement

Src/C_AMRLib/INTERP_3D.F

commit 21353eb59ea6f4ef48088a3a7803744bf8d8af49
Author: lijewski <lijewski>
Date:   Thu Mar 24 20:37:37 2011 +0000

    some OMP refinement

Src/C_BaseLib/SPECIALIZE_3D.F

commit 2140cb837261be7410fbdecf6466f6d2791996a7
Author: lijewski <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 8e36d2b91ba4644c9d591a08d6b1338f7930bd44
Author: lijewski <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 260f9bf32f587a4506fc589c30ca791a3227d4e1
Author: lijewski <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 66488df6e0ed070dd1cbc5c48dc2bd07c34a8c07
Author: almgren <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 2417f0eab67ab7cb83ff6577fd634cd19cdf9267
Author: almgren <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 a362034c826b262715bea55938327e4ed16cd339
Author: almgren <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 8750d3d4279eab462a7444e63f4b6ae853669717
Author: almgren <almgren>
Date:   Sun Mar 20 15:29:42 2011 +0000

    Fix typo.

Src/LinearSolvers/F_MG/ml_cc.f90

commit bb3be359ed62d543b91ca7d4911ad760002341e4
Author: almgren <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 063c6ec9b2274f439875dc176434a318f5e413a4
Author: almgren <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 46db06e6f82a444333a9ce83d20e1024f688bde0
Author: almgren <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 fb822cea060a2e912c938c110a1862e9f07a2c38
Author: almgren <almgren>
Date:   Sun Mar 20 02:51:00 2011 +0000

    Need to allow for nghost > 1.

Src/F_BaseLib/create_umac_grown.f90

commit f9dc28eec61dc7ec015c1d09241399ed26d688e1
Author: almgren <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 297f684479389da634491e64e33c31b70a8ded84
Author: almgren <almgren>
Date:   Sat Mar 19 01:24:04 2011 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit d1dbfe9f37d9e7113cf9cabfc14398deaf3ece97
Author: almgren <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 9359d5c6dc4c8cec356c27bcafc1c05463c31dbd
Author: lijewski <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 ee4a5a8651742057c8e25f24146a4e06187e49a5
Author: lijewski <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 cd7454eb59e27aedd83f089737e3277f2cf7ac22
Author: lijewski <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 338fa647ea9003dd64569043104e88ba2d70dbea
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:13:01 2011 +0000

    removed some too-little-work OMP loops

Src/C_BaseLib/COORDSYS_3D.F

commit 7cb36dbe8cf80a87ad378e3939e0184f2cad4a0e
Author: lijewski <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 e45a546d4b670e0e183fa89a21dd282247465ddc
Author: lijewski <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 cf12f0a8b1f6afb20e7224f7d33d0a609218a5e5
Author: almgren <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 cb72fe9926711677eedeae9acc0d26ef2e478288
Author: almgren <almgren>
Date:   Wed Mar 16 17:56:35 2011 +0000

    Convert is_singular from integer to logical.

Src/LinearSolvers/F_MG/mg.f90

commit 1238084fb571304a614ebc13ff7909b733aa9963
Author: almgren <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 40b92c9e79cf0ce927c3400d4cee847ecad57683
Author: nazgul <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 6496454e9463a50842fd81c2ce5cbc287a7ebc6b
Author: nazgul <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 4c3e728e0161dbe06274a5b75cc6e81392a75362
Author: almgren <almgren>
Date:   Thu Mar 10 23:42:04 2011 +0000

    Add pleiades stuff.

Tools/C_mk/Make.mpi

commit 9e9ac222bf00746da9d412e516df37b71c8d2bc3
Author: wqzhang <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 4b563eed384008f151d3235e57a095a77236ec48
Author: ajnonaka <ajnonaka>
Date:   Wed Mar 9 13:32:07 2011 +0000

    typo in output string

Src/F_BaseLib/fab.f90

commit 1fab0e02a30478beff2acdf79d2552cdc498545a
Author: almgren <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 6d3094e5eb4a2a731ec26e7bda3ba216e6cd4935
Author: marc <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 9ecdc4aedd638a06172ec165897fb7626e0f93c4
Author: lijewski <lijewski>
Date:   Tue Mar 8 02:09:14 2011 +0000

    little mod to previous OMP reorg of estTimestep()

Src/C_AMRLib/Particles.H

commit 4aab43cc31ace18a6bb5c04a9eded8087e4e5c8e
Author: almgren <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 171bf8c3b5dadfed8fa9a3f5b279ae3457681b91
Author: almgren <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 02f7c6714f89e5586e6cd22edea08ad77c615748
Author: almgren <almgren>
Date:   Sun Mar 6 16:20:48 2011 +0000

    Move ParallelReduceMin call out of verbose test.

Src/C_AMRLib/Particles.H

commit f1567c7e7770472db7365c2186d2c4f66bbd3ba9
Author: lijewski <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 9d338e55bff0d3407bde7b00de2d0a98f19a8929
Author: almgren <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 9430028f28312307619eb0a47c2d9f7be5df49ff
Author: almgren <almgren>
Date:   Thu Mar 3 23:19:38 2011 +0000

    Verbose --> SetVerbose

Src/C_AMRLib/Particles.H

commit decf8586bec23f742edaddc1499f895f8e468496
Author: lijewski <lijewski>
Date:   Thu Mar 3 21:49:55 2011 +0000

    some simplification

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit e6a410050705544b3b60dfeec67952ab99c15833
Author: lijewski <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 c74965304bea2fd785d803cc4dcab168128ff377
Author: almgren <almgren>
Date:   Wed Mar 2 23:21:49 2011 +0000

    Comment out print statement.

Src/LinearSolvers/F_MG/mg.f90

commit 10148680c4c97961f463e4165a46c14023c7afa5
Author: almgren <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 36697343c540ba3bbe0bd08a25d1fc3f7a6b86f1
Author: almgren <almgren>
Date:   Wed Mar 2 23:20:11 2011 +0000

    Fix print statement.

Src/LinearSolvers/F_MG/itsol.f90

commit 092c96ddaf873fa943cc8539db1e5c38770ddd59
Author: lijewski <lijewski>
Date:   Tue Mar 1 17:12:29 2011 +0000

    simplified AdvectWithUMac()

Src/C_AMRLib/Particles.H

commit 0056194423bd84c11fb7a3cc76dcafccf9587a00
Author: lijewski <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 15359151ffd1f62f4bf3351fd19c2bd95ad3e180
Author: wqzhang <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 a13afe27106e45a63ad41d932f6795067f69cbfc
Author: wqzhang <wqzhang>
Date:   Mon Feb 28 23:05:34 2011 +0000

    *** empty log message ***

Tools/C_util/regtests/radiation-tests.ini

commit 76a3ed532b637df8bb0aa26f49d7ce6664960dfa
Author: lijewski <lijewski>
Date:   Mon Feb 28 21:17:26 2011 +0000

    removed an assertion

Src/C_AMRLib/Particles.H

commit a276abdc90f9e195149013cbb196e5a02abbcef6
Author: mzingale <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 202d43019f5c85f7d01c68bccb5a2139f59fa87f
Author: lijewski <lijewski>
Date:   Mon Feb 28 19:03:52 2011 +0000

    bit more simplification

Src/C_AMRLib/Particles.H

commit da99837d45613ef4482d2618c7b632c60bf486b1
Author: lijewski <lijewski>
Date:   Mon Feb 28 18:29:09 2011 +0000

    made AdvectWithUMac mirror the one in fParallel

Src/C_AMRLib/Particles.H

commit bd814a9861ef552906b13e2be881a40a82f8d862
Author: lijewski <lijewski>
Date:   Mon Feb 28 18:23:43 2011 +0000

    some cleanup & speedups

Src/C_AMRLib/Particles.H

commit b9113d8337669d092906e46006a0853485e8aec2
Author: lijewski <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 8191987436b691a83be2c3d0b44392f01b1a57a1
Author: almgren <almgren>
Date:   Sat Feb 26 01:59:18 2011 +0000

    Remove extraneous definition.

Src/C_AMRLib/Particles.H

commit ecc0a32a9959a6a70cf29f4974e0bcfe780e25bd
Author: almgren <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 ad32e4b18ad64991c9fab3090ac95b174b138847
Author: almgren <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 fb3267b96504790cbf9114432ed804ad6e612f4b
Author: almgren <almgren>
Date:   Sat Feb 26 00:03:02 2011 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/itsol.f90

commit fefb50e6c1ecbb58b1e9eca675c6d0eb832d2911
Author: lijewski <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 c793cbf2566a0a9c93f73be7c84d2414b61ef9fc
Author: lijewski <lijewski>
Date:   Fri Feb 25 22:13:25 2011 +0000

    contains_nan_bx_c()

Src/F_BaseLib/fab.f90

commit a3d1537258146a33d020563b145f6e36506e7a97
Author: lijewski <lijewski>
Date:   Fri Feb 25 21:17:51 2011 +0000

    contains_nan_allc() calls contains_nan_c()

Src/F_BaseLib/fab.f90

commit e36f505e3c905f7fad735cc980c7be3560d18892
Author: lijewski <lijewski>
Date:   Fri Feb 25 21:10:52 2011 +0000

    added contains_nan_c()

Src/F_BaseLib/fab.f90

commit b93d6a7a7c8466b1876e10bd823070d8bb651734
Author: lijewski <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 c49682e5717c7fac9d38eb694ad23efbe4d5dc7a
Author: mzingale <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 da0d39fa20dcefb72658a32b5d48935ef5baf468
Author: marc <marc>
Date:   Thu Feb 24 01:06:52 2011 +0000

    *** empty log message ***

Tools/C_util/ViewMF/viewMF.cpp

commit e754a154e1dac939fcfac94c9d6b6f582d01dc57
Author: almgren <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 b36e5e07bc95c3c7939f8f8501c320f080f8bc64
Author: almgren <almgren>
Date:   Tue Feb 22 23:35:14 2011 +0000

    Fix test for mgt%bottom_singular.

Src/LinearSolvers/F_MG/mg.f90

commit 1f9b10ee9111e8f17ed96979b312899e9e3c0565
Author: almgren <almgren>
Date:   Tue Feb 22 21:48:34 2011 +0000

    Change Init --> InitFromAsciiFile

Src/C_AMRLib/Particles.H

commit d45146841a13d705b7e98791a1c4fdd1fb895f7e
Author: mzingale <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 ec735c5b5208b57c5f092168b512eb147dc51d28
Author: almgren <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 51144f0206314ae2ae58bcb35f4851d7493c869c
Author: lijewski <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 3b36953818e096536b48b416dda94b38e019bddd
Author: lijewski <lijewski>
Date:   Thu Feb 17 00:02:18 2011 +0000

    changes to debugging interface

Src/F_BaseLib/particles.f90

commit c6e4a3ec1522655239e36a34ebb70909961d1567
Author: almgren <almgren>
Date:   Tue Feb 15 22:38:43 2011 +0000

    Forgot commas.

Src/C_AMRLib/Particles.H

commit 753ee107fdb96631044fe272a7221382d1aeb404
Author: almgren <almgren>
Date:   Tue Feb 15 22:33:16 2011 +0000

    Fix typos.

Src/C_AMRLib/Particles.H

commit 9394334f629e51ba6f0b717fb83a604194b0425a
Author: almgren <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 8fc6d3eca6346901387f6f3105a1b9b0525c57a9
Author: almgren <almgren>
Date:   Mon Feb 14 22:54:12 2011 +0000

    Add adot/a term to velocity update.

Src/C_AMRLib/Particles.H

commit 7ab13319272884efdfb1dd609bc5cf471d6fe963
Author: almgren <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 5ea376fad0c0bc6ca9c9c91f1f0874fbc18e2e5e
Author: almgren <almgren>
Date:   Sat Feb 12 03:17:19 2011 +0000

    Integrate changes from Test_90Mpc version.

Src/C_AMRLib/Particles.H

commit 066b496b2a4796e883fe18819873e5977d101b86
Author: lijewski <lijewski>
Date:   Fri Feb 11 22:30:02 2011 +0000

    some cleanup

Src/C_AMRLib/Particles.H

commit 9820e1f703baf3a36fe4a23f3c1230bb75cac6dc
Author: lijewski <lijewski>
Date:   Fri Feb 11 21:50:34 2011 +0000

    added WriteAsciiFile()

Src/C_AMRLib/Particles.H

commit 1d6773edf0754278edf55f8a080d31b38690523e
Author: marc <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 010fb60a7449ae71ff633bee3e6da4771022f54c
Author: lijewski <lijewski>
Date:   Thu Feb 10 00:06:50 2011 +0000

    fixed issue with Timestamp()

Src/C_AMRLib/Particles.H

commit 1ff197a7cb6f3337b5fa9804d447a74eb7483db5
Author: lijewski <lijewski>
Date:   Wed Feb 9 23:42:03 2011 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.H

commit 57f06b41befa0fc1f1a752e1f01028e414d7934d
Author: lijewski <lijewski>
Date:   Wed Feb 9 23:21:15 2011 +0000

    some work on advectWithUMac()

Src/C_AMRLib/Particles.H

commit 83c98742ce84a1905af56178698809277970cc01
Author: lijewski <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 1d44bf67d4d27d058c79bae2d2c0465d9939e85d
Author: lijewski <lijewski>
Date:   Tue Feb 8 22:17:50 2011 +0000

    redistribute() now also does the origpos member

Src/F_BaseLib/particles.f90

commit 052bcb45974fa501ff0ed58d83c0092e9194cfa8
Author: lijewski <lijewski>
Date:   Tue Feb 8 19:19:01 2011 +0000

    more work on Timestamp()

Src/C_AMRLib/Particles.H

commit 36eb78f73485bf89f1f96d44a7cc8a3c47ba30a6
Author: lijewski <lijewski>
Date:   Tue Feb 8 19:05:22 2011 +0000

    some work on Timestamp()

Src/C_AMRLib/Particles.H

commit 7a69276e0928c2ca225efff9391fc149c702b7f0
Author: mzingale <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 1cfb9ac8ad1c1ae641b8d97119a85d1194f99025
Author: lijewski <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 6960604d56982e3e3fbb58049e5e484292412061
Author: lijewski <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 2cfae6126c8237ca57b5fe4377a9969e9e6b0d65
Author: lijewski <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 02f2c51091b16cac95b89a7e25e9056b5b0a0f2d
Author: lijewski <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 4acd736c44b3b951520540649ff01ee07e5b942d
Author: lijewski <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 cad83c1ba8cd1f9cb47aac175a46aeeb2614cb55
Author: lijewski <lijewski>
Date:   Fri Feb 4 20:25:50 2011 +0000

    deal with N==0 in InitRandom()

Src/C_AMRLib/Particles.H

commit 867b8e4a8f06c421dd131642830d82bc7a18e736
Author: lijewski <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 ff551c5253d92b019f881f7f72467910e0fa265f
Author: lijewski <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 f348386750a4d0bd3884c3b7e9b6e9ad2cffc26c
Author: lijewski <lijewski>
Date:   Fri Feb 4 16:44:00 2011 +0000

    added a BL_ASSERT()

Src/C_AMRLib/Particles.H

commit a6554e10ec5e1caad6739693d43e7edb3965f299
Author: lijewski <lijewski>
Date:   Wed Feb 2 22:15:45 2011 +0000

    removed do_not_minimize_comcost stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 9830644617668bc960cb40591b21d0c51cad79ab
Author: marc <marc>
Date:   Wed Feb 2 01:42:16 2011 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit d67e0c21e31df0b528985988a96fac7237e98e22
Author: mzingale <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 06ea0c878ba9ce8b551458e43e009a3afd35397b
Author: mzingale <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 408c4522f7929a2efce9b4e3d8584fb55af9c67d
Author: ajnonaka <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 8c2407bad4bcf8e1c88c0ce7d659b5d3cfb2f247
Author: ajnonaka <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 97e1496134e7c74ea31aea6c69149b3b6aa78985
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 28 00:41:26 2011 +0000

    bilinear advection using MAC velocities (2d only)

Src/F_BaseLib/particles.f90

commit 83cc07e9c5753d9619fac59f1a2bd69c664a4ed5
Author: ajnonaka <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 41ca636b59e63f22e4efe77aad6599abaea74390
Author: lijewski <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 88e22e618409a8333cc601f0068d151f6c30dd83
Author: ajnonaka <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 72bf41f600bebec44a17159202e75078708fc2db
Author: lijewski <lijewski>
Date:   Thu Jan 27 23:19:50 2011 +0000

    more error checking

Src/F_BaseLib/vector_i.f90

commit fa8f593fc9616dc5f4966014c84ab1502fcca930
Author: ajnonaka <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 793278eba90fa491451c1700430cbda0d7ad5bee
Author: ajnonaka <ajnonaka>
Date:   Thu Jan 27 22:46:20 2011 +0000

    added an advect function

Src/F_BaseLib/particles.f90

commit b1a6fee9ddc2360255388a11909ccc22ba729490
Author: lijewski <lijewski>
Date:   Thu Jan 27 22:31:22 2011 +0000

    more error checking

Src/F_BaseLib/particles.f90

commit 35f05e1a007215f81547ec8626771855d560e5e3
Author: lijewski <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 bfa95841f2da0da4ed46702ea06218a3c7ab52e4
Author: lijewski <lijewski>
Date:   Thu Jan 27 21:27:57 2011 +0000

    mods for MAESTRO

Src/F_BaseLib/particles.f90

commit 6866556f33baf7fb91c16945f77e21e4ca35f720
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:51:02 2011 +0000

    now used PARTICLES

Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit 1285bb4c4c58dc32908a701abd338f6dd8e34598
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:47:07 2011 +0000

    added PARTICLES macro to get particles.f90

Src/F_BaseLib/GPackage.mak

commit 2e934edde00f0f3d9a3bf1b2d32a8e9dda91978c
Author: ajnonaka <ajnonaka>
Date:   Wed Jan 26 21:12:13 2011 +0000

    add f90sources += particles.f90

Src/F_BaseLib/GPackage.mak

commit d849e3d80066fb6d26b492e6e4a11bb8a7297d8e
Author: lijewski <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 5f5cc418453a3f337ce32dd1ffcf39aa448fab68
Author: marc <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 7d08a25cee9226319a770ea2ef94b9741b8a2e6d
Author: lijewski <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 4ebccc21f7bb4011b7ced2ed8b13d84b684f0322
Author: lijewski <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 9fb9e098439849a193b915a77f9de94eb3481a18
Author: lijewski <lijewski>
Date:   Tue Jan 25 18:44:57 2011 +0000

    some simplification

Src/F_BaseLib/particles.f90

commit d92e7996959a376a82a072f19bf92cefafe82cd3
Author: lijewski <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 35e9855c36bd1ed7f42db8fa70416f5cf4ca70e7
Author: lijewski <lijewski>
Date:   Tue Jan 25 00:04:21 2011 +0000

    little more cleanup

Src/F_BaseLib/particles.f90

commit 0f896f5a3aba2be62728f1dbb7af198072d3ccfa
Author: lijewski <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 79ef8c32de4a6213608aa3beef55499fada19c6f
Author: lijewski <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 d6d7dc83cd692cbb73efd79b19245942e8789f77
Author: lijewski <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 6ec088427b03ea52a928dac38310433f83c5a081
Author: lijewski <lijewski>
Date:   Mon Jan 24 23:07:58 2011 +0000

    some cleanup

Src/F_BaseLib/particles.f90

commit 021d126a42e06a6e43fda6ba19a08a3b77525559
Author: lijewski <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 54d069772cf48b2306577dbe051ca8db4f071152
Author: lijewski <lijewski>
Date:   Mon Jan 24 22:35:42 2011 +0000

    timestamp() appears to be working

Src/F_BaseLib/particles.f90

commit 0f7ddc22273de44115b69ad2e0c4f401da0845af
Author: lijewski <lijewski>
Date:   Mon Jan 24 22:22:58 2011 +0000

    timestamp() closer to working

Src/F_BaseLib/particles.f90

commit 898c78342a8d04421dfe68d74c30163260100b1f
Author: lijewski <lijewski>
Date:   Mon Jan 24 21:06:56 2011 +0000

    *** empty log message ***

Src/F_BaseLib/fabio_c.c

commit 4b5bb86d2e0a5ee6047f1df56fbbc3be424cfaa2
Author: lijewski <lijewski>
Date:   Mon Jan 24 21:06:42 2011 +0000

    some work on timestamp()

Src/F_BaseLib/particles.f90

commit aba76452d148a3eaf5be20f6ffcd719bfe701216
Author: lijewski <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 4b83cf01f208d667245d775dbb9c9bb0f2294713
Author: lijewski <lijewski>
Date:   Fri Jan 21 21:22:03 2011 +0000

    some cleanup

Src/F_BaseLib/particles.f90

commit 2441c7cd9e3f2518891ae362536ba7606894bffd
Author: lijewski <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 7030025520e245ae5235288524be68abd3e5da4e
Author: lijewski <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 044e7d90f94dfff32fca14b036ff582e22995735
Author: lijewski <lijewski>
Date:   Fri Jan 21 20:51:52 2011 +0000

    restart appears to be working

Src/F_BaseLib/particles.f90

commit fcca1e3fd4b895f6df52a11e8f6188b29d8bcab3
Author: lijewski <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 9871b024787e61946e720fe2cd9ae7a60e7a6ecc
Author: lijewski <lijewski>
Date:   Fri Jan 21 01:21:16 2011 +0000

    some work on restart()

Src/F_BaseLib/particles.f90

commit 4b6f198a27c4aef8959451569b13b7d43f183fbf
Author: lijewski <lijewski>
Date:   Thu Jan 20 21:35:32 2011 +0000

    checkpoint() appears to work; on to restart()

Src/F_BaseLib/particles.f90

commit c79367e01c3fc2391384cc432fbf2077a8e7c719
Author: lijewski <lijewski>
Date:   Thu Jan 20 17:45:26 2011 +0000

    checkpoint() is that much closer to working

Src/F_BaseLib/particles.f90

commit 1a749d52cf690a1b196db1855cfa168733844d87
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:51:18 2011 +0000

    yet more work on checkpoint()

Src/F_BaseLib/particles.f90

commit 450135d72fb4b5ba7fef6838e460637b0d1371a7
Author: lijewski <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 bc08374707f7d752c7d84dcc564a0e2fec807e4b
Author: lijewski <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 9e24f9c5cdac9615d00d72524827b101e998e4fa
Author: lijewski <lijewski>
Date:   Wed Jan 19 23:37:09 2011 +0000

    yet more work on checkpoint()

Src/F_BaseLib/particles.f90

commit 34dcae34170bea43e7b92dec38a9c329b6cd59fa
Author: lijewski <lijewski>
Date:   Wed Jan 19 22:26:51 2011 +0000

    some more work on checkpoint()

Src/F_BaseLib/particles.f90

commit 8cdcacccae1f1647f43f1cd93eda3b1cb634e4fc
Author: lijewski <lijewski>
Date:   Wed Jan 19 21:43:22 2011 +0000

    some work on checkpoint()

Src/F_BaseLib/particles.f90

commit 9ec9f68ce28ddd092ba66882784c3cf9c1eb6a96
Author: lijewski <lijewski>
Date:   Fri Jan 14 21:25:30 2011 +0000

    comment out particles.f90 for the moment

Src/F_BaseLib/GPackage.mak

commit 93978bc12db39de004a594cb45e8a76b11dd6b48
Author: lijewski <lijewski>
Date:   Thu Jan 13 19:13:20 2011 +0000

    redistribute() appears to be working

Src/F_BaseLib/particles.f90

commit 1d16e087d9af21bdea2ef33d825558b8cea78886
Author: lijewski <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 30e05579aaf617425fb672e77b5c121959a16c0d
Author: lijewski <lijewski>
Date:   Thu Jan 13 18:15:16 2011 +0000

    redistribute() is closer to being working code ...

Src/F_BaseLib/particles.f90

commit 453f37c586d59f6365a2480b90c614b24648a513
Author: lijewski <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 48e34c80d7cb5e84e5ea5031ad2d89b90d4951e6
Author: lijewski <lijewski>
Date:   Thu Jan 13 00:18:13 2011 +0000

    some work on redistribute() - not finished

Src/F_BaseLib/particles.f90

commit a9d924603278973e37859a737133446a3b96936e
Author: lijewski <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 ba7c173e60df7c00d98e57de52f52ca0b592772d
Author: lijewski <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 1b2347d1c4da8f4d71ab1431290bf8324aa62bbc
Author: lijewski <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 8999d5e16a4add74b3bbadea3f72e70003053d94
Author: lijewski <lijewski>
Date:   Wed Jan 12 17:55:14 2011 +0000

    multi-level mla's appear to work OK

Src/F_BaseLib/particles.f90

commit 6c817629eb7e53c96f2be62febd0acf6e78a5a95
Author: lijewski <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 ccf577809346848cc3e1be7ab8c8beb5d37c6418
Author: lijewski <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 a03164472ba68378ddaeed2b239e8285a917e04a
Author: lijewski <lijewski>
Date:   Wed Jan 12 00:27:26 2011 +0000

    init_random() seems OK in serial

Src/F_BaseLib/particles.f90

commit 923d7e6ca349840a4ffe1bf2b07d14e3e70ae79e
Author: lijewski <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 aa975c19008193677954d44d80e56f47c79f15db
Author: lijewski <lijewski>
Date:   Tue Jan 11 23:56:23 2011 +0000

    wrote init_random() -- untested yet

Src/F_BaseLib/particles.f90

commit 62ac6b9ba8e33f889b5a6a296bbd59002f792f1e
Author: lijewski <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 4741b3debed1f30e50351d26aac42d2c8df8237c
Author: lijewski <lijewski>
Date:   Tue Jan 11 20:30:22 2011 +0000

    particle_vector knows about valid/invalid particles

Src/F_BaseLib/particles.f90

commit f888ec5ee834e8fa45a3860a134526806ed96609
Author: lijewski <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 7ecddec52432edff84f7e76a9819106a43558dff
Author: lijewski <lijewski>
Date:   Tue Jan 11 18:25:28 2011 +0000

    added particle_vector

Src/F_BaseLib/particles.f90

commit b45cfa8f81244d0c5747c32b722e0c943e7a335b
Author: lijewski <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 7187ab287dbac198d273661d2a4d6fa044b84375
Author: lijewski <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 7df9d2c335f29bb3c16a334955ada3c6a6eae26c
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:01:11 2011 +0000

    added particles.f90

Src/F_BaseLib/GPackage.mak

commit 6ae26882e0b475619250202303e23ac8433f00cc
Author: lijewski <lijewski>
Date:   Tue Jan 11 17:00:47 2011 +0000

    Just getting started ...

Src/F_BaseLib/particles.f90

commit 64c1d3862458024004442155d8f2cf2b0b97e817
Author: almgren <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 51f3b9ce40e031405c8b2f71b4957fb01bb0195f
Author: almgren <almgren>
Date:   Mon Jan 3 21:35:05 2011 +0000

    Add a to estTimestep.

Src/C_AMRLib/Particles.H

commit ebc94aee6ffa46230fbc9b0164d9a56f5e83d9f7
Author: almgren <almgren>
Date:   Mon Jan 3 20:49:31 2011 +0000

    Fix...

Src/C_AMRLib/Particles.H

commit 31b31408a973951dcb0d24121e82f67b01115f51
Author: almgren <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 88dfccf64427cde51113d91593b48d8c155df152
Author: almgren <almgren>
Date:   Mon Jan 3 20:26:30 2011 +0000

    This doesn't compile.

Src/C_AMRLib/Particles.H

commit 8e1334a37bdbb336830e3048bcaece46e08d5bd0
Author: gpau <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 579daae447b79f8d1183eb25fe5d804c67dd06f0
Author: ajnonaka <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 465bb870714fc6f6519d22f82aea45b4ef957654
Author: mzingale <mzingale>
Date:   Tue Dec 21 15:08:41 2010 +0000

    add toy_convect, diffusion tests

Tools/C_util/regtests/Maestro-tests.ini

commit a6a07dcba5ae940060a93e13f0596349e5a4f4f0
Author: ajnonaka <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 03b256c4a36107e180f05bf4bc0f9cd07b125f6f
Author: mzingale <mzingale>
Date:   Wed Dec 15 03:30:51 2010 +0000

    trap uninitalized variables in debug mode

Tools/F_mk/comps/gfortran.mak

commit a3e47d18e0b145233f82ce31c689d3ebb8655278
Author: mzingale <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 1325df76afc9c5339e28f66e0b26cf8d87cc15e1
Author: gpau <gpau>
Date:   Thu Dec 9 00:53:21 2010 +0000

    fix for pgCC oddity

Src/C_BaseLib/BaseFab.cpp

commit 374d27fce8038d14e4faba493b13804d2b208625
Author: lijewski <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 036231f5daaf6f9d3090afe33eb79df3b15bfd09
Author: lijewski <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 6a8feccc1f719d6873cb062e6f0e6f1c81f57a91
Author: lijewski <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 e732667011ef231c471b2532675631b13930bd3e
Author: lijewski <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 ec85ba75a9371d680b3013013628e270f7d00e0d
Author: mzingale <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 f69e436e21ac9b11d005b06fb86d2e38b8454b9e
Author: lijewski <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 fd20966736ec945991c5d2f935be1bd8de576fad
Author: lijewski <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 7db322e0c33adf87ea5259dbb0a8b5cbcfc773a7
Author: ajnonaka <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 05404c58f1e98116b48e7d38fabe731a15428d41
Author: lijewski <lijewski>
Date:   Mon Nov 15 19:23:57 2010 +0000

    speedup to InitRandom()

Src/C_AMRLib/Particles.H

commit 1b89204fbe3c20a24c26cba5c7a3d30b510c3599
Author: vince <vince>
Date:   Mon Nov 15 19:13:37 2010 +0000

    couts.

Src/C_AMRLib/StationData.cpp

commit b933c1cfd4a3bd039cc5c22bcc9473b6fa2826e4
Author: lijewski <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 7d99a64c37a7ca3d9974035bc5888343d6f3e361
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 11 17:54:39 2010 +0000

    fixed USE_OLDPLOTPER

Tools/C_mk/Make.defs

commit c487c7ea18909f44d52c84abcbb8be44bdd4cf25
Author: ajnonaka <ajnonaka>
Date:   Thu Nov 11 17:48:44 2010 +0000

    add support for USE_OLDPLOTPER=TRUE in makefile

Tools/C_mk/Make.defs

commit 34369ca97c3ba3e73a92211c3ec8f0bc8ea282d2
Author: ajnonaka <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 02dd446f78166bcd17ce12630371a1b19c074d7f
Author: lijewski <lijewski>
Date:   Wed Nov 10 23:46:48 2010 +0000

    tweaked g++ and gfortran debug options

Tools/C_mk/Make.defs

commit 1345fa56321794813488e188b608c0527ac649c6
Author: lijewski <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 9167678d102c90c47100a7e321ac5e7b8d0d4e95
Author: lijewski <lijewski>
Date:   Wed Nov 10 22:10:08 2010 +0000

    more IPM tweaks for hopper and franklin

Tools/C_mk/Make.Linux

commit 033096e841d50e7a21c561b3158036cc549a053f
Author: lijewski <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 2660b6291fbfc131c30598c42f176702ca130c61
Author: lijewski <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 4a4c4fe8ce364e5eca939e821ee61f4560158136
Author: lijewski <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 279aae3f83ed5b9662287e2a5e3067404e02d102
Author: almgren <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 85e8d8da31fc9e6555fe38c7a9f7aced53c7704a
Author: lijewski <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 e565151be781216367652085e44261672b07cfc2
Author: almgren <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 c867217aa35191665c089d2a6385ced44aaa8f6b
Author: vince <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 ef14bef657b09c81e30124fc24cf11ae6c7127e8
Author: vince <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 699fe61c3f1ae8069ff6966165f8ff59c5722a6b
Author: lijewski <lijewski>
Date:   Fri Nov 5 21:00:44 2010 +0000

    fixed bug I just introduced

Src/C_AMRLib/Particles.H

commit cbf6d34a7e961f36ab118895ae89819a809fb00d
Author: lijewski <lijewski>
Date:   Fri Nov 5 20:13:53 2010 +0000

    trimmed memory use in Redistribute() a tad

Src/C_AMRLib/Particles.H

commit 185a0cfc994214c4a95c611fe536573fe8ee52d4
Author: lijewski <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 804466f78aef5fa6b846a803a595b0cd6b475807
Author: lijewski <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 f7bba288baf7e4a7172a95fa384693a164975748
Author: lijewski <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 a697c679a831cf74b0dff3b290b77fe7e4ef1f8b
Author: lijewski <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 c05dcae3cb69182f673112946762a2586c46404c
Author: lijewski <lijewski>
Date:   Thu Nov 4 16:24:40 2010 +0000

    some more error checking

Src/C_AMRLib/Particles.H

commit 72684afbb7ea1d69c108c2be628bc0b1caabba89
Author: lijewski <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 03cfa026aedfd1b53d7e5714e4fd664b104a50f0
Author: almgren <almgren>
Date:   Tue Nov 2 16:05:37 2010 +0000

    oops -- still need variable "vol"

Src/LinearSolvers/F_MG/mg.f90

commit 35e75225395922a487a61b0f97ea2f6e2cedd7bd
Author: almgren <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 25cc8a815e055be39ccaebcc3168c8e3b68c0ffa
Author: lijewski <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 aec28d67e7f334a4e9b25d5b3c7b13bf300ed745
Author: lijewski <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 586ca3793a51584d0851a6b0d9cac2c3a56f8c58
Author: lijewski <lijewski>
Date:   Mon Nov 1 20:57:00 2010 +0000

    some performance tweaks

Src/C_AMRLib/Particles.H

commit 1411cd0485927f1ccc044b8c42d92bec954246a9
Author: lijewski <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 a1ad4cf64a59656d72ef5a3dd01078d059ce9316
Author: lijewski <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 d19ced8db8759c2eebb1f081dc83ad53039e3d3a
Author: lijewski <lijewski>
Date:   Mon Nov 1 17:16:55 2010 +0000

    some IPM stuff for hopper

Tools/C_mk/Make.Linux

commit 47ca92460b111674f4b5d94becda416ff765a1e9
Author: lijewski <lijewski>
Date:   Fri Oct 29 22:50:41 2010 +0000

    added ability to sort particles -- not yet used

Src/C_AMRLib/Particles.H

commit a6fa5c893abd0df8c0afa1a12ca5befd26f5ae00
Author: lijewski <lijewski>
Date:   Fri Oct 29 21:39:15 2010 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_cc.f90

commit a2c528428bd15616e30532d2804d593174dfe61c
Author: almgren <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 c48e6f06d2e7deea90b8b8ce9aa34d363ca26dc9
Author: lijewski <lijewski>
Date:   Fri Oct 29 20:36:14 2010 +0000

    added serialize option to InitRandom()

Src/C_AMRLib/Particles.H

commit cfc48b8c917be36dbd1916c32244601c3487c94d
Author: lijewski <lijewski>
Date:   Fri Oct 29 17:22:04 2010 +0000

    *** empty log message ***

Src/C_AMRLib/Particles.cpp

commit f04e94647d924f0b86d67bb2697966e103f18156
Author: lijewski <lijewski>
Date:   Thu Oct 28 15:56:43 2010 +0000

    AssignDensity() wasn't quite right for 3D

Src/C_AMRLib/Particles.H

commit 18b725b8bcda7dbb56df45c31bbfbfcbb6d4519f
Author: lijewski <lijewski>
Date:   Wed Oct 27 22:11:54 2010 +0000

    tweak to OMP in sumParticleMomentum() to satisfy PathScale

Src/C_AMRLib/Particles.H

commit ec14ab52c77f77de9612859f440a38f5aa76b585
Author: lijewski <lijewski>
Date:   Wed Oct 27 22:04:34 2010 +0000

    simplified the OMP scheme for sumParticleMomentum()

Src/C_AMRLib/Particles.H

commit c0be065d433ff7206653b04546d57843466d59eb
Author: lijewski <lijewski>
Date:   Wed Oct 27 21:56:03 2010 +0000

    OMPd sumParticleMomentum()

Src/C_AMRLib/Particles.H

commit 6c71f397461189c44936765f7589601fc906dbca
Author: lijewski <lijewski>
Date:   Wed Oct 27 21:25:55 2010 +0000

    came up with a way to OMP AssignDensity()

Src/C_AMRLib/Particles.H

commit 4f77026d5e1d9ae2e142ecc6fb83b16143f0f820
Author: lijewski <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 7147d6d4df1f54bebf1a3ee384f9305cffbc7946
Author: lijewski <lijewski>
Date:   Wed Oct 27 19:41:04 2010 +0000

    mods for PathScale

Tools/C_mk/Make.Linux

commit bdad9c9db4e9791b17a284014f50d4f75c999017
Author: lijewski <lijewski>
Date:   Wed Oct 27 17:44:22 2010 +0000

    added -h noexceptions to CXXFLAGS for Cray

Tools/C_mk/Make.Linux

commit b1b6fdf4ad66889c8acd6a673de04d14d4be4806
Author: lijewski <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 50cb0c483c41abc87c84e7504980646c89b7e4d7
Author: lijewski <lijewski>
Date:   Tue Oct 26 22:09:17 2010 +0000

    decrease Cray optimization intensity

Tools/F_mk/comps/Linux_cray.mak

commit d4920dca1894f54daeab5f9d1d4ab55866f7be26
Author: lijewski <lijewski>
Date:   Tue Oct 26 20:32:29 2010 +0000

    decreased Cray optimization strenght a bit

Tools/C_mk/Make.Linux

commit 37ea3ac68239abae316e19e779681be14dda8cce
Author: lijewski <lijewski>
Date:   Tue Oct 26 20:21:33 2010 +0000

    mods to quiet Cray compiler

Src/C_AMRLib/Particles.H

commit 07cd56f74dc3254a03fc14b2803a8eafef3b7fee
Author: lijewski <lijewski>
Date:   Mon Oct 25 23:36:18 2010 +0000

    OMPd estTimestep()

Src/C_AMRLib/Particles.H

commit c4a4a983120c88fd4d38b98599d585c908efc45f
Author: almgren <almgren>
Date:   Mon Oct 25 22:10:07 2010 +0000

    Fix indexing of cell vs csect in AssignDensity...

Src/C_AMRLib/Particles.H

commit 1ab78da01b160aa4f93efe85c8031bae44458634
Author: almgren <almgren>
Date:   Mon Oct 25 22:01:54 2010 +0000

    Fix up getGravity

Src/C_AMRLib/Particles.cpp

commit ea4151f491c61752ed04bf2154e7c0c6da9319ce
Author: lijewski <lijewski>
Date:   Mon Oct 25 20:06:33 2010 +0000

    getParticleGrav() -> ParticleBase::GetGravity()

Src/C_AMRLib/Particles.H
Src/C_AMRLib/Particles.cpp

commit bc9b83affba9cf1d6d06b23603a9612fda7fcf16
Author: almgren <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 1f411ab5e706032e5236e50e2841e5c98331dac5
Author: lijewski <lijewski>
Date:   Mon Oct 25 03:43:11 2010 +0000

    little cleanup

Src/C_AMRLib/Particles.H

commit f5b55c0106b7f82a58ab9190abb2768d9cb5b0f7
Author: lijewski <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 93fa83226be2bfa117a889822b14469c41e0657a
Author: lijewski <lijewski>
Date:   Sun Oct 24 23:41:46 2010 +0000

    some OMPing

Src/C_AMRLib/Particles.H

commit e635c870b4448a70ab4dac1c69dc1fe9d5d206ca
Author: lijewski <lijewski>
Date:   Sun Oct 24 22:45:29 2010 +0000

    minor performance tweaks

Src/C_AMRLib/Particles.H

commit cca09a3d9e373142bc5a6ea774c47e8b775c1da0
Author: lijewski <lijewski>
Date:   Sun Oct 24 22:07:10 2010 +0000

    add some more timers

Src/C_AMRLib/Particles.H

commit 93dd81491112a8d4f981c4ac2a84ca66fd7d6203
Author: lijewski <lijewski>
Date:   Fri Oct 22 23:25:30 2010 +0000

    more Cray tweaks

Tools/C_mk/Make.Linux

commit 905dfc24b8ffe0a8f42647826c940eb8d59a25b9
Author: lijewski <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 e1657e8780492c6b131425518e5ab0363a8bc622
Author: wqzhang <wqzhang>
Date:   Fri Oct 22 21:10:12 2010 +0000

    added my desktop baragon

Tools/C_mk/Make.defs

commit 0e402335de03e6053d27995301edb225ad3ede17
Author: ajnonaka <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 39a5d403027d92d8511243cce596dd95caa8ac5a
Author: lijewski <lijewski>
Date:   Fri Oct 22 20:26:10 2010 +0000

    more Cray stuff

Tools/C_mk/Make.Linux

commit a13bca42cf898079677b3f48306161ac0cdb0a10
Author: lijewski <lijewski>
Date:   Fri Oct 22 16:48:51 2010 +0000

    some work adding Cray

Tools/C_mk/Make.Linux

commit 9c23cefc5becaf4f9ddf14596cdbbde5dd1e02de
Author: lijewski <lijewski>
Date:   Fri Oct 22 15:34:29 2010 +0000

    added -Minline flag

Tools/F_mk/comps/Linux_pgi.mak

commit 4ef1e55f01d7c94cd9f361a0d1368cc49eefec44
Author: lijewski <lijewski>
Date:   Thu Oct 21 20:59:14 2010 +0000

    for Cray compilers

Tools/F_mk/comps/Linux_cray.mak

commit 23bfbc8384952aa45d81521cd5e875d0623800cc
Author: lijewski <lijewski>
Date:   Thu Oct 21 20:58:15 2010 +0000

    some work for Cray compiler suite

Tools/F_mk/GMakedefs.mak

commit 458676a5bc634ed2fe47221592611def53bb0222
Author: lijewski <lijewski>
Date:   Thu Oct 21 18:21:39 2010 +0000

    added grace

Tools/F_mk/GMakeMPI.mak

commit a7630a69256ac207b765a5083d213abc2aec4d75
Author: lijewski <lijewski>
Date:   Wed Oct 20 23:17:09 2010 +0000

    tweaked the PGI optimization flags

Tools/C_mk/Make.Linux

commit 91681b72b57cd0563234dd5dd65122bd4d351003
Author: lijewski <lijewski>
Date:   Wed Oct 20 23:15:22 2010 +0000

    added GRACE

Tools/C_mk/Make.defs

commit 3f9e34e18ef417cecc487e3f0bfb6e1e9023923b
Author: ajnonaka <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 699296f89d4ed42db03736a3b17026b94be5905f
Author: mzingale <mzingale>
Date:   Wed Oct 20 13:54:55 2010 +0000

    add support for kraken

Tools/F_mk/GMakeMPI.mak

commit 7c420e6e21e12e9649a374d8e5e74486d4b84472
Author: wqzhang <wqzhang>
Date:   Tue Oct 19 22:48:32 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.rules

commit 4b376771d07635394baab35c6afa0828d8735aba
Author: ajnonaka <ajnonaka>
Date:   Tue Oct 19 00:04:05 2010 +0000

    MPI for ebirah

Tools/F_mk/GMakeMPI.mak

commit 8cd95fd8565f30cabfbffc2ea871f888e325b795
Author: almgren <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 ace12b459ae4b24b7d2745b50db5ffff0dbe7ea0
Author: lijewski <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 9a35210d1497cb72a784cc678f6fe38308ae7e37
Author: lijewski <lijewski>
Date:   Mon Oct 18 20:02:18 2010 +0000

    some performance tweaking

Src/C_AMRLib/Particles.H

commit bda8decbfcdff2146d2da8902586ef1350b5fb27
Author: lijewski <lijewski>
Date:   Mon Oct 18 19:18:49 2010 +0000

    a little cleanup

Src/C_AMRLib/Particles.H

commit db5fb9fb0efc49201208e70543857f2f9f65cfef
Author: lijewski <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 013e613060d25cc8d542de14a26907c7d325b6ec
Author: lijewski <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 004ff2311d1908247127d054adbda22004db6c90
Author: almgren <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 7f608cec15614f1082fb79c0e8653bcc4eda43aa
Author: lijewski <lijewski>
Date:   Fri Oct 15 21:33:53 2010 +0000

    some cleanup and additional error checking

Src/C_AMRLib/Particles.H

commit b854f15dc32230b27c87df5b3c79466eb057217e
Author: ajnonaka <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 78923cd35cbdf8f7659201c36e6cfda0655992c0
Author: lijewski <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 b55e7a415384e47da6873af4ea4f89da0509f478
Author: almgren <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 2a7f7eea5b928a7131b1b517fd52e5feffeee16f
Author: adonev <adonev>
Date:   Fri Oct 15 20:21:27 2010 +0000

    Added flag BL_FAST_COMP

Tools/F_mk/comps/Linux_intel.mak

commit 8dc3a14ee9a109cd64d6653045cc2af22a62ee5b
Author: lijewski <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 87caa7bf7c1ea44598dc176ff63a227ab20897f0
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:50:37 2010 +0000

    a little cleanup

Src/C_AMRLib/Particles.H

commit 45e68c8b71ca3d6e3e4369cbbaccbb043c1ace5e
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:34:34 2010 +0000

    OK() is now more thorough

Src/C_AMRLib/Particles.H

commit 9d86b374ab6e6c178e1a53b52f4c279a74c2aff7
Author: lijewski <lijewski>
Date:   Thu Oct 14 23:13:04 2010 +0000

    yet more work on Checkpoint()

Src/C_AMRLib/Particles.H

commit 1901783cc450c81f58f807063abfe267caac1212
Author: lijewski <lijewski>
Date:   Thu Oct 14 22:37:31 2010 +0000

    more work on Checkpoint()

Src/C_AMRLib/Particles.H

commit dbdc78e5254ed57695365cf084ac4b2da54e3a42
Author: lijewski <lijewski>
Date:   Thu Oct 14 21:51:03 2010 +0000

    initial work on Checkpoint(); more needed

Src/C_AMRLib/Particles.H

commit 0db3ea4f12eaddbbb0809f4e00acdc346cc9b3f6
Author: lijewski <lijewski>
Date:   Thu Oct 14 17:34:43 2010 +0000

    some optimization

Src/C_AMRLib/Particles.H

commit e1e161c89abb3539f0d89d8cfe8a7ce980b13ad0
Author: lijewski <lijewski>
Date:   Wed Oct 13 23:11:33 2010 +0000

    some cleanup and more error checking

Src/C_AMRLib/Particles.H

commit 19da4fae4dbce31813ada5b8abdd6d93ddf385c0
Author: almgren <almgren>
Date:   Sat Oct 9 19:16:31 2010 +0000

    Add verbose to test for output...

Src/C_AMRLib/Particles.H

commit 2e5835f505ed67597d8e274eb0125e3653e04345
Author: almgren <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 e934ce022e92adde473b015de4df04a970ca81e0
Author: almgren <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 01aedbaf9ba4d00404a2b11408ea8cff334c3207
Author: almgren <almgren>
Date:   Fri Oct 8 17:03:28 2010 +0000

    Latest updates from JF.

Src/C_AMRLib/Particles.H

commit c4dd3d4cdac940584afca35cea9e3aea32fa48be
Author: almgren <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 14be603f02e57e14d5d56ace2f81f9c1921ffe88
Author: almgren <almgren>
Date:   Wed Oct 6 22:05:14 2010 +0000

    Add Particles_F.H

Src/C_AMRLib/Particles_F.H

commit 607c40956248a34d97f16680d7fc731eaf37fbc2
Author: almgren <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 96368a67b4f244f36c8b6a89cad845f35f54be9d
Author: almgren <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 f85de47915842a1a30059f2029f0a1584019a21b
Author: vince <vince>
Date:   Wed Oct 6 20:01:22 2010 +0000

    added new machines.

Tools/C_mk/Make.mpi

commit 511263a4974b7133f05af6222fe4e21554ac6ace
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:44:20 2010 +0000

    little code rearrangement

Src/C_BaseLib/FabArray.H

commit 84db0fa66d0d581fee32c4472da7c7cbe41574bd
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:38:30 2010 +0000

    little code rearrangement in SumPeriodicBoundary()

Src/C_BaseLib/Geometry.cpp

commit 8f2776af708cd403e1689171c5cf6d75fd41f067
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:31:30 2010 +0000

    use intersections() in SumBoundary()

Src/C_BaseLib/MultiFab.cpp

commit b43e60333e519c5657418237ca9ad78df52e03c9
Author: lijewski <lijewski>
Date:   Wed Oct 6 15:14:27 2010 +0000

    minor code motion

Src/C_BoundaryLib/BndryData.cpp

commit a6bcb87153b36fa75e39bc10f1e927c37577f6b2
Author: lijewski <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 69546ec70e6e895ec5ad788986bb81c7e6ab7b7e
Author: lijewski <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 16b40b9b494ae663ace6f023435eddf830d0aca6
Author: lijewski <lijewski>
Date:   Tue Oct 5 21:40:47 2010 +0000

    added SumPeriodicBoundary()

Src/C_BaseLib/Geometry.H
Src/C_BaseLib/Geometry.cpp

commit 3b8a0190c893b5af2cc924186ecb477fda6235d4
Author: lijewski <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 a9a7faeef0afa168f4ea1309a29d8c478eeb1c5b
Author: adonev <adonev>
Date:   Sun Oct 3 23:32:29 2010 +0000

    donev in Makefile

Tools/C_mk/Make.mpi

commit 31b7045112f1462cc91fc27aedf25736d708377a
Author: ajnonaka <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 23e75b9be1ebcd018f6ee2dc90ba54843a11099c
Author: ajnonaka <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 f292b253025921032f52e0efc5fe82ca09a42718
Author: marc <marc>
Date:   Fri Oct 1 21:55:40 2010 +0000

    Add win include

Src/C_BaseLib/IntVect.H

commit 2cdac7e3efe399cd82753f55be39b6181f5ff63f
Author: marc <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 17c95e390429d07c689ea084567d095d16b13ac9
Author: ajnonaka <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 bed6cb58df43b10043b1f7df7c1a0f77fc6b0708
Author: lijewski <lijewski>
Date:   Fri Oct 1 21:44:47 2010 +0000

    brought back from the dead

Src/C_BaseLib/GNUmakefile

commit 4271dd0d25039be17c88c19493127403652ef89d
Author: ajnonaka <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 40ca155204a341b50e2fdaa8fb8a44cea0b38f1a
Author: ajnonaka <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 e234e1b5a2b8cbb770c967e20e53f6b47d235982
Author: ajnonaka <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 a35d17cfd95db2d325cc07b034f7d13be65518b4
Author: almgren <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 0342844f3301c1c76d8a972a83c729b7bcb8b865
Author: lijewski <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 0b6cb900ceffd9fef061e8b8ab3f730545e67ce0
Author: ajnonaka <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 14e011b1a93a61b2599c6691acf69f3f27f95e95
Author: ajnonaka <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 e4de48465afea8d24e4ff137eea33692f8a46e3c
Author: marc <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 8831c4a3be3348ba3ed6256fb59f3a2e467273c1
Author: marc <marc>
Date:   Wed Sep 29 23:14:21 2010 +0000

    Incorporate name changes into filelist

Src/LinearSolvers/C_NodalMG/Make.package

commit b616ca28d54b3c79a7cbcebde0b9942b91ae0cf2
Author: marc <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 670c8477cc7c2fa740c8cc49da4e13f02cc7f89f
Author: marc <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 4f9d253e0df25142f4d4b2f5ae7522e3ca0b5f0a
Author: marc <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 06493f646345bd241f1e34e293b1801843977a17
Author: marc <marc>
Date:   Wed Sep 29 03:46:35 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit e4efb88b979d73acac5a9e78584b90b09663daac
Author: adonev <adonev>
Date:   Mon Sep 27 23:28:22 2010 +0000

    Added host donev

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 22bbfe0b44f13da00d39ddea4e266bb4ae8d3dc9
Author: adonev <adonev>
Date:   Mon Sep 27 21:22:18 2010 +0000

    Added host donev

Tools/C_mk/Make.mpi
Tools/F_mk/GMakeMPI.mak

commit a529bc8014dfc340cb4ec2ee2c3e2977f3c2a3ef
Author: lijewski <lijewski>
Date:   Mon Sep 27 21:11:33 2010 +0000

    more particle stuff

Src/C_AMRLib/Make.package

commit 6ad5817ec0aec986897d5ee9a9fcfa875e04d24f
Author: gpau <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 a003a1e01bddf388fa6b50603da9b5432caedaae
Author: gpau <gpau>
Date:   Tue Sep 21 22:01:10 2010 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit f052c129196931bb6cb4e9c3379cddac6cbaa545
Author: wqzhang <wqzhang>
Date:   Thu Sep 16 21:29:17 2010 +0000

    Fixed a comment

Src/C_BaseLib/IntVect.H

commit b2ddf346fc1da0ad0a51d2c00b01830ec865f426
Author: ajnonaka <ajnonaka>
Date:   Thu Sep 16 17:56:36 2010 +0000

    Chris' fix to get PathScale working on atlas

Tools/F_mk/GMakeMPI.mak

commit ccaa62ebc2d682073546dbe4929e8ab99f75949c
Author: marc <marc>
Date:   Mon Sep 13 20:33:30 2010 +0000

    fix PathScale second underscore thing

Tools/C_mk/Make.Linux

commit 8616318751812416775435c75a6d1d28d93612ba
Author: lijewski <lijewski>
Date:   Fri Sep 10 23:05:34 2010 +0000

    beefed up FULLWARN for g++

Tools/C_mk/Make.defs

commit 2a135e619f582121cd4a6988f5b452ab898c2811
Author: lijewski <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 6930f58a911770263d0f9b4898805b4b65b454a6
Author: lijewski <lijewski>
Date:   Fri Sep 10 20:24:52 2010 +0000

    added -fbacktrace flag when debugging with gfortran

Tools/F_mk/comps/gfortran.mak

commit 280fa58ae08981cf5c75b518c0da0c5c38562150
Author: lijewski <lijewski>
Date:   Thu Sep 9 16:47:29 2010 +0000

    unOMPd setval()

Src/F_BaseLib/fab.f90

commit da39749fe0f526ee4032b9d7d1841b6241123632
Author: lijewski <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 17fab4f6bbc51ad420af20c838767766b856ab93
Author: almgren <almgren>
Date:   Wed Sep 8 16:47:35 2010 +0000

    Add kraken stuff.

Tools/C_mk/Make.Linux

commit 75299b5aaa380d8f736336f058a00f5bd82ae564
Author: almgren <almgren>
Date:   Wed Sep 8 16:46:48 2010 +0000

    Add kraken info.

Tools/C_mk/Make.defs

commit 288527260ed37727f60ba77a76adff9c22c514ce
Author: gpau <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 530f5b60ccbbecc813fa1128035cb165d6592e97
Author: almgren <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 d419c5bd440786ef295861e542094b5a1c1a7c02
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 31 15:21:08 2010 +0000

    MPI on my home machine

Tools/F_mk/GMakeMPI.mak

commit ed3928691807dabe708f0a130afb668967f8be1e
Author: ajnonaka <ajnonaka>
Date:   Tue Aug 31 15:21:01 2010 +0000

    MPI on my home machin

Tools/C_mk/Make.mpi

commit 94ea214989b8f8d259bfb9bc078f636f402344c1
Author: ajnonaka <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 f760fe9bd0adab2ae59b62183702e80e741eb376
Author: ajnonaka <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 106038a8f392307314d17c84788482f812339fb9
Author: ajnonaka <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 68767687a2bae8161b462edbf1e18f2d44e89b7d
Author: almgren <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 c6fd0dc65ac69db837f93550c5e95a395fcf8dbc
Author: ajnonaka <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 2abb2890caf57d98b13068cc8e48168e40976d54
Author: nazgul <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 f7bca0357aeb645235d6c68ee788f76328cc54ee
Author: lijewski <lijewski>
Date:   Wed Aug 25 21:40:17 2010 +0000

    no longer include sparse_solve.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit cf043347ab65831b2c24d608708888521da14feb
Author: lijewski <lijewski>
Date:   Wed Aug 25 20:37:51 2010 +0000

    removed some dubiously useful OMP constructs

Src/LinearSolvers/F_MG/ml_util.f90

commit 56e332685e1d7ae171aa2b68e85d7e6a81a7a47c
Author: lijewski <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 7e3f458a6ba9318d893f5cfa6a331a49a7f3d49d
Author: lijewski <lijewski>
Date:   Wed Aug 25 19:35:15 2010 +0000

    OMP'd stencil_norm() when present(mask)

Src/LinearSolvers/F_MG/stencil.f90

commit 9b1b1172a2be3fc91fa1e66beab8f36a73652e40
Author: lijewski <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 f62a514ed549f31d8f3a5b7c68bbe77e92a01b96
Author: ajnonaka <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 633071250b98233ca062c7702039e247f9fb40b9
Author: almgren <almgren>
Date:   Tue Aug 24 20:30:31 2010 +0000

    end if --> endif

Src/C_BaseLib/BoxLib.cpp

commit 948a8181a1ab1b84861173c2cdd2f79df15e666d
Author: almgren <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 c71e59a2892ba6c87bbb753ad133a7384aedb603
Author: lijewski <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 aead63ff2827ad21c6d2e6fc91aa046f4657852a
Author: almgren <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 6300eabc2e5d75855bfa71bac75a666abafe998d
Author: lijewski <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 b852c5281e3c582ddd70405faafac9471a44cf5a
Author: lijewski <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 dcce444829a4570fa6c1c7ec79bdc600270f1cd2
Author: ajnonaka <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 2d2d0344bb9cc50e4f9c46c533d85151d710b448
Author: lijewski <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 c8dbe1da99619aadc5550ab71647657d25eb28ee
Author: ajnonaka <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 fcde7f4c4f9ffdabebf01d41337639d2d15f4b1c
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:30:30 2010 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_solve.f90

commit 75264e4526a635be0f582142cb4cc35f90b3ef62
Author: lijewski <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 b1f5c864cb35752d502e90a06ea2cc34638b33ae
Author: lijewski <lijewski>
Date:   Fri Aug 20 16:46:50 2010 +0000

    some more OpenMPing

Src/LinearSolvers/F_MG/stencil.f90

commit cbb3f9129ec1b20a47999d2a0d74040a938aea74
Author: lijewski <lijewski>
Date:   Thu Aug 19 23:45:25 2010 +0000

    removed some unused routines & made some private

Src/LinearSolvers/F_MG/stencil.f90

commit 1aedf33e9ebf227cc2db640b8abde257b4256294
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:56:32 2010 +0000

    refined public interface

Src/LinearSolvers/F_MG/nodal_mask.f90

commit abce4934d0c8e2b38882933f6a43fd0070face59
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:36:40 2010 +0000

    fixed up public/private stuff

Src/LinearSolvers/F_MG/ml_restriction.f90

commit ffd6875881d636878306772a6ee9a1f8e16e83ef
Author: lijewski <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 add76ce0ccca76e56a74db4043e276a9ec0fed39
Author: lijewski <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 9c3012093c84031db79e9512be0d6c94f863b70b
Author: lijewski <lijewski>
Date:   Thu Aug 19 22:12:30 2010 +0000

    make scale_residual_[123]d private

Src/LinearSolvers/F_MG/ml_cc.f90

commit b733db4d7b564b8b496c2a4b96b7fd6cf74ed7df
Author: ajnonaka <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 f3a8c0644ac02096d97e5b5f331c0d897355289e
Author: lijewski <lijewski>
Date:   Thu Aug 19 21:30:06 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/itsol.f90

commit 12db264079513f77842aca5df518a844f2f9ca1f
Author: lijewski <lijewski>
Date:   Thu Aug 19 21:19:17 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/nodal_newu.f90

commit c2ca381fe5a736f8c7a960aa1c543b2470e4b461
Author: almgren <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 fb7ba108b94f8c48c628ca1d9ff989381f050e8b
Author: lijewski <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 3bc6ca71589b6d5b2b298298cc1f661737e34c38
Author: lijewski <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 1f9999920509e1e48203de4ed7d0f890263467b7
Author: ajnonaka <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 f529a0652e527cf96d8670dcb5fd0cb7f65f184a
Author: ajnonaka <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 768c329836d3e9910e439d34c5dde29de36139ae
Author: lijewski <lijewski>
Date:   Mon Aug 16 20:02:11 2010 +0000

    plugged memory leak

Src/F_BaseLib/fabio.f90

commit 9f20a9685cb3dca6826a968f191a97940b7bf33b
Author: lijewski <lijewski>
Date:   Mon Aug 16 19:26:22 2010 +0000

    shut up some valgrind warnings

Src/F_BaseLib/bndry_reg.f90

commit ec7573d0b1f10478f3c43ea78f63d873fd290c3e
Author: mzingale <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 3e4445a08c5e8ff823b768b1ba5872f57e023d51
Author: lijewski <lijewski>
Date:   Fri Aug 13 21:44:26 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f5909642f1be94b2ac895b3b519aebf612712de9
Author: lijewski <lijewski>
Date:   Fri Aug 13 20:30:07 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 93d7cc34ac04c5b387cc57f3b3fb1852c738db87
Author: lijewski <lijewski>
Date:   Fri Aug 13 20:18:08 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 235bc7141a3efa55d6b93a9dfd61b4c9010c5249
Author: lijewski <lijewski>
Date:   Fri Aug 13 17:21:51 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/mg_restriction.f90

commit ac1170ad718d735b52e887551d751fdfac8a491a
Author: lijewski <lijewski>
Date:   Fri Aug 13 17:05:32 2010 +0000

    some OpenMPing

Src/LinearSolvers/F_MG/coarsen_coeffs.f90

commit d8115d3ce0ecd124f90f247e6a8e97ad018e4e48
Author: lijewski <lijewski>
Date:   Fri Aug 13 16:33:13 2010 +0000

    some code rearrangement

Src/F_BaseLib/sort_box.f90

commit 84fd7fda33c261f086f02367cc4ff828f37de640
Author: lijewski <lijewski>
Date:   Fri Aug 13 16:24:31 2010 +0000

    some OpenMPing

Src/F_BaseLib/interp.f90

commit 7a5724bcaef7a86c3b2c99f5387bedb3f16c7603
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 13 15:16:41 2010 +0000

    test commit for cvs email notifications

Src/F_BaseLib/make_new_grids.f90

commit 0c065b307246b062d6891a15cd85d9e697f00001
Author: ajnonaka <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 270506f74cc54425835d77af9509ef8dd8cd2f26
Author: lijewski <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 68df84af8b8ed585a3bb0004ddf51c6cc24f18f5
Author: lijewski <lijewski>
Date:   Thu Aug 12 23:18:05 2010 +0000

    removed bl_nd_interp_[23]d

Src/F_BaseLib/interp.f90

commit 04727810ce3db68b9660ee9a939db3fb771e6eb6
Author: ajnonaka <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 fa80329fb991143c3f8ff4cb806d042c245c665d
Author: lijewski <lijewski>
Date:   Thu Aug 12 21:04:28 2010 +0000

    workaround for dumb IBM xlf bug

Src/F_BaseLib/fillpatch.f90

commit 9ac4e5bbd69ee842341ff8b6d31e911a5c275c99
Author: almgren <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 27442eb5fcee8b83fcf01e45eadd65d8d95c3bc1
Author: lijewski <lijewski>
Date:   Thu Aug 12 19:33:22 2010 +0000

    OpenMP'd min_val and max_val routines

Src/F_BaseLib/fab.f90

commit 137c2ed9ce257fdf2665a91e100af3cd945fdeaf
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:41:18 2010 +0000

    OpenMP'd sub_sub and plus_plus routines

Src/F_BaseLib/multifab.f90

commit e64eb4a9ad58d404d6b171e3ad45f61cd5939bda
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:27:38 2010 +0000

    OpenMP'd mult_mult routines

Src/F_BaseLib/multifab.f90

commit db8184d4b6064a02e8cd7e1799eaead3a813f394
Author: lijewski <lijewski>
Date:   Thu Aug 12 17:18:03 2010 +0000

    OpenMP'd div_div routines

Src/F_BaseLib/multifab.f90

commit a4d2edb5c42597baa843218cbc6f502fe6b583e3
Author: lijewski <lijewski>
Date:   Thu Aug 12 16:06:17 2010 +0000

    some code simplification

Src/F_BaseLib/multifab.f90

commit 32e769269f1937067db055c2af65f4851c0e5b43
Author: ajnonaka <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 f8cde24b29bfc48463754ea652ef950ffbd41b44
Author: gpau <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 a6fd2824e5f01a149aee7ff2e14fd692c208307b
Author: gpau <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 cc935fbedc36cbdebfee17a6fbaa1b3b1e343394
Author: mzingale <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 d74844a335cee80c066ec6987ca371b3055ea0af
Author: lijewski <lijewski>
Date:   Thu Aug 5 15:53:24 2010 +0000

    compiles now

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 5a5504cd03d6a27df34c4739ccf6d3a3c947fe3b
Author: mzingale <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 fbfce1f4a2588d011ebbd40604b435af5888fd42
Author: almgren <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 c30a693f25bd562d7bf5d757cfb5589515bf8180
Author: almgren <almgren>
Date:   Fri Jul 30 21:41:06 2010 +0000

    Fix an oops.

Src/C_AMRLib/INTERP_1D.F

commit 0648074cad647b19fe4cc50f139b8a05b36e1de8
Author: almgren <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 3560d96bb960dc04d12ef3ff8c256fd9b6ad7fd9
Author: almgren <almgren>
Date:   Wed Jul 28 01:21:08 2010 +0000

    Fix another oops.

Src/C_AMRLib/INTERP_2D.F

commit 614aaa2b1b195a02cdc8ed9ace8b7825a0eec4e0
Author: almgren <almgren>
Date:   Wed Jul 28 01:17:57 2010 +0000

    Typo before.

Src/C_AMRLib/INTERP_2D.F

commit ecbd4f7d285d43683bbc93e4d5bddab649cea6b5
Author: almgren <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 7892155f2b42a8896fbe2a110431f3d6b2f39494
Author: gilet <gilet>
Date:   Wed Jul 28 00:50:55 2010 +0000

    Change MPIHOME for orga so things work again

Tools/F_mk/GMakeMPI.mak

commit 54cfa6c50806b21948b13362670dc528cb037e08
Author: almgren <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 d682444a61747a68c93cd9e970e9e26941ba6ff0
Author: almgren <almgren>
Date:   Mon Jul 26 16:54:04 2010 +0000

    Start to put use_hypre option in.

Src/LinearSolvers/F_MG/mg.f90

commit 0c2520bde636838695c6004491e9be49310db696
Author: lijewski <lijewski>
Date:   Fri Jul 23 23:14:46 2010 +0000

    some g++ and gfortran mods

Tools/C_mk/Make.defs

commit 12d9a7694994a00fb095b85b7df1caf711ea3b2b
Author: lijewski <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 4a718b26437a0fc6d76bdbc903f3251ee6cbcb28
Author: lijewski <lijewski>
Date:   Fri Jul 23 17:00:40 2010 +0000

    add -fopenmp if OMP

Tools/F_mk/comps/gfortran.mak

commit c009f2485aef70b297639721d1facb70a618a8c6
Author: almgren <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 586b7f289003f23304fbb13db2cf249b9c337fde
Author: almgren <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 05259a44efb44ac89894ab46f66ae869596f4203
Author: almgren <almgren>
Date:   Fri Jul 23 03:19:20 2010 +0000

    Fix oops in previous commit.

Src/LinearSolvers/F_MG/ml_nd.f90

commit 10a57ecc550b01be6c19940edf4b3efc3255839f
Author: almgren <almgren>
Date:   Fri Jul 23 03:15:47 2010 +0000

    Add print statement if already converged

Src/LinearSolvers/F_MG/ml_nd.f90

commit d33b8837317f565c552dc1c3792c230a8f8249a2
Author: almgren <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 3ee6a3fff3a7fb6686a868cd72b8329decb3ef11
Author: almgren <almgren>
Date:   Thu Jul 22 14:34:43 2010 +0000

    Removed quotes around included files.

Tools/F_mk/GMakedefs.mak

commit 332ba211461c98717ed36890a2bdec33e80e48fb
Author: almgren <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 688401ca2be2c3e8b5d086e794d32db098513474
Author: almgren <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 06076f617dd72c1d1d521555506d037e6509e23b
Author: lijewski <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 d188e8d8ff880681b76a2a4e57dd693caaf6b527
Author: lijewski <lijewski>
Date:   Wed Jul 21 19:03:55 2010 +0000

    fix for when not all levels defined

Src/F_BaseLib/ml_layout.f90

commit 6b1ff2c853bfd29076935c9fe25fc4c76112e1bb
Author: almgren <almgren>
Date:   Tue Jul 20 21:35:12 2010 +0000

    Need this to compile from C++

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 4b356fb143c8bf8eb176c7edb4363861377f246e
Author: almgren <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 348fea521c6137a2d91838db07bd637364ff3be7
Author: almgren <almgren>
Date:   Tue Jul 20 19:58:40 2010 +0000

    More clean-up of use modules...

Src/LinearSolvers/F_MG/ml_solve.f90

commit 8fbdb79edeec394b40c24143fb11a71737743bbd
Author: almgren <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 3da572b38f5636596f2699b1e9167b75a102044e
Author: almgren <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 5acedd98a7eaa6d4268bf054b57cc213c30bc831
Author: almgren <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 3893c6099a08b3ced41adb5713c6c0e90a328177
Author: almgren <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 2e7b2e8a5c0dcc9cef947bf358f3a2ab09b74533
Author: almgren <almgren>
Date:   Tue Jul 20 19:22:48 2010 +0000

    Fix oops.

Src/LinearSolvers/F_MG/ml_nd.f90

commit fc6339d8696449edb78644a106bba15c130a780e
Author: almgren <almgren>
Date:   Tue Jul 20 19:03:17 2010 +0000

    Fix oops...

Src/LinearSolvers/F_MG/ml_nd.f90

commit 6870145a34ee6a7af7092655f459abb4604f1051
Author: almgren <almgren>
Date:   Tue Jul 20 19:00:09 2010 +0000

    Moved grid_res into ml_nd.

Src/LinearSolvers/F_MG/mg.f90

commit 650b29936e4679bca828e0b6e0ffcd7777f9ce43
Author: almgren <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 c26ffedf0f98dcd86e6ace782a760706cb7649a4
Author: almgren <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 6c692b19a5c7d37ad54bfb65f7a1275698716ee8
Author: almgren <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 7de3f2e7fa8bdaf6503112b1daf4fbae9b56c67c
Author: almgren <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 8d6ae70b18c4613c83b24aa25f8de4c8fd63bcc9
Author: almgren <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 02776ef2fc19210bd881213473c300b8a4922ac9
Author: lijewski <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 bf9109579442238f2a52804c72cdb701211c503b
Author: almgren <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 dad9ca4052b81694ee8731f89872c7bd8a5f4f4d
Author: almgren <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 85b97bd0ac0b3758c5fb150ba4aa0675f54b6ccd
Author: almgren <almgren>
Date:   Mon Jul 19 18:10:08 2010 +0000

    Works now for ranger.

Tools/C_mk/Make.Linux

commit 10ebef18880b0ff7b8bea5825bb64503af8391dc
Author: lijewski <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 9a5ecdc99746f5cb492ef1b28cc61ffceb1ac04f
Author: lijewski <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 917247d1ffbb5f87afa7f1712306acab12c6ae38
Author: lijewski <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 666b36f825891a0ddb4366ef72c699eff62b6984
Author: lijewski <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 198ba5378c9520d82d19b64e1c8a9f4fda9b3c3c
Author: almgren <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 77ef622690ebf5464a76049b6ccf9ca7331116ac
Author: lijewski <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 dee5a7e22a171bd5a0ef3f8a820c58c1b8ddf6a7
Author: lijewski <lijewski>
Date:   Wed Jul 14 20:16:18 2010 +0000

    made get_dim() a pure function

Src/F_BaseLib/box.f90

commit 139e5286590c8c4e86bc6255fac581d1d196660e
Author: lijewski <lijewski>
Date:   Tue Jul 13 22:16:48 2010 +0000

    made component types private

Src/F_BaseLib/bl_stream.f90

commit 2f93ad35bf355820cc73303239e5094ebaa43bc1
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:22:53 2010 +0000

    made a couple module variables private

Src/F_BaseLib/plotfile.f90

commit 3512c203840b1dd7127d3a1e3b49592159d2b32d
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:22:33 2010 +0000

    removed pingpong.f90

Src/F_BaseLib/GPackage.mak

commit 3d3a038ecff7df32c8d71224f2802e55a4e2b4ed
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:15:56 2010 +0000

    made sfc_greater_i() private

Src/F_BaseLib/knapsack.f90

commit 4943188442707a67f61f2bb5857ec04210135869
Author: lijewski <lijewski>
Date:   Tue Jul 13 21:04:17 2010 +0000

    made a module variable private

Src/F_BaseLib/bl_timer.f90

commit 85daf2d11d92a0ef1a2aaafe823ac89b31449549
Author: lijewski <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 0cbbbf71b51898046c52f49793a0351c4bb16a16
Author: lijewski <lijewski>
Date:   Tue Jul 13 20:50:49 2010 +0000

    removed unused module variable

Src/F_BaseLib/box.f90

commit a0f4a9d8b22e1a267d923257cb9b256f999d6cac
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:50:53 2010 +0000

    only call simplify() if too few grids

Src/C_AMRLib/AuxBoundaryData.cpp

commit 9b8bc4edb19aabde5e9296160d67a155e9ef5b8e
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:35:46 2010 +0000

    add back in KnapSack to initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 7d84ce28ab6600533fa1d8b08a500d043899f971
Author: lijewski <lijewski>
Date:   Wed Jun 30 22:16:36 2010 +0000

    do a maxSize() after the simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 436d9889ccc3eb41433db5c13e5eb4d04532231c
Author: lijewski <lijewski>
Date:   Tue Jun 29 20:19:45 2010 +0000

    sped up boxlist_simplify() and boxarray_simplify()

Src/F_BaseLib/list_box.f90

commit fb611f234fbec0253720af8ab8cc4d2544153ca3
Author: ajnonaka <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 a2bdfd1461d66245919e06fe13282777822c5df2
Author: lijewski <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 f261d602c5d1d03ab4d017c019ef2241405f6501
Author: lijewski <lijewski>
Date:   Mon Jun 28 18:25:12 2010 +0000

    initialize() now calls GetBndryCells()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 5f4750bb48d68d4995608c8c0a3fbc690d698d1a
Author: lijewski <lijewski>
Date:   Mon Jun 28 18:24:45 2010 +0000

    make better use of faster simplify() in GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit 6152aaaf743a0dcbf25e1e41a0931e285f3c2ae0
Author: lijewski <lijewski>
Date:   Mon Jun 28 17:43:50 2010 +0000

    call simplify() at end of GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit e0a6aa956b42920221d989bae361b56be6e34ab8
Author: lijewski <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 f832bf9539fa06ea554ad29a733e5ee53aaf7f16
Author: lijewski <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 be162ecc613dbaa5ed37d14a164c23c74c7416e3
Author: vince <vince>
Date:   Fri Jun 25 22:36:07 2010 +0000

    added some diagnostics and a sync.

Src/C_BaseLib/VisMF.cpp

commit f7093103802a3a469f200452208587f268ff244f
Author: lijewski <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 07dcb53541dc506d6c096f8f16d9138e270e3f6b
Author: almgren <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 5fc7cd4ae88fb229c3ee8153454d38081fa4f2e3
Author: almgren <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 32b9050471b0c62d0bc0bd566e353f63e8e645e5
Author: almgren <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 f33e821c05c018f4955ac87561d4cdef5ef5eb28
Author: lijewski <lijewski>
Date:   Fri Jun 18 22:22:05 2010 +0000

    more refinement of refine_grid_layout

Src/C_AMRLib/Amr.cpp

commit fb308d5f6a9d7e4b5cb9cf51f74224c097d55054
Author: lijewski <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 21fc8d074789a602345a6ea51473dcacd2f265e6
Author: lijewski <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 4573eefbfd458609851992bfcb988c495ce86bd2
Author: almgren <almgren>
Date:   Fri Jun 11 19:48:58 2010 +0000

    Add kiryu.

Tools/F_mk/GMakeMPI.mak

commit a4f46996848194ecfb20a3878e155569d49764f4
Author: marc <marc>
Date:   Thu Jun 10 20:29:13 2010 +0000

    Mods for marcs account on the TUe computer

Tools/C_mk/Make.mpi

commit 807caec85cdc7d5c96116828d085217aaf14da5e
Author: almgren <almgren>
Date:   Thu Jun 10 00:34:46 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit b94f519160d2b0107ab62258b16d145fea0775f3
Author: almgren <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 de0d9ae6e7a7576b83a243ff360d4b09dbdb1bde
Author: mzingale <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 bad0b869f2ca6b65b7a8654390e671fffab95280
Author: gpau <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 45aa055d33f7b474b0982a519693124bc2ba4852
Author: mzingale <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 06f81c33d6a171a524e012d4acd1d4843216e94a
Author: almgren <almgren>
Date:   Tue Jun 8 21:34:32 2010 +0000

    Dont maintain NPackage.mak anymore.

Src/F_BaseLib/NPackage.mak

commit fd58b47053d7a7e206235190f628afd8b37ee173
Author: ajnonaka <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 c0d61a746ad1bc56b7253cd6e8b6979df9d9efa2
Author: almgren <almgren>
Date:   Mon Jun 7 19:59:39 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/stencil.f90

commit c2cfc2830adec2ba7ccaa9de6bbe407652c6013e
Author: ajnonaka <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 9d4865fef2d1307504c3a5f4f1ba6bdf90d03da0
Author: almgren <almgren>
Date:   Sun Jun 6 20:07:22 2010 +0000

    Fix this.

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 4f0f78eecc34870a072a443c35e1bf0928caf49d
Author: gpau <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 af14fd8be6fbe1adf7653393df5ff8cc459c870a
Author: gpau <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 4ceaae39e5da9e6933f2afad201bf220087a2069
Author: adonev <adonev>
Date:   Fri Jun 4 23:16:23 2010 +0000

    Added host angilas

Tools/F_mk/GMakeMPI.mak

commit 875838b5c50696da5f9afefa0f170f81456b4f25
Author: almgren <almgren>
Date:   Fri Jun 4 21:42:45 2010 +0000

    Latest ...

Docs/BoxLib/boxlib.tex
Docs/paper.tex

commit 0018f85531179f9d6087f582c455cdf243d5bc9e
Author: almgren <almgren>
Date:   Fri Jun 4 21:39:28 2010 +0000

    We just keep making it better...

Docs/BoxLib/boxlib.tex

commit 4aaaa0ed59ab94573b55782276e2fa8a46293122
Author: almgren <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 a042e68e6ca78b9e2547aee98ed8ccb33f7ea43d
Author: almgren <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 3cd8e4513d1b942b9554c798ac09d141b2a981e7
Author: almgren <almgren>
Date:   Fri Jun 4 21:15:33 2010 +0000

    For now this holds the copyright info.

Docs/preface/preface.tex

commit e012340200140644f5615c8c1bc1bfcc764f129b
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 4 17:14:31 2010 +0000

    works now for array of regrid_int's

Src/C_AMRLib/Amr.cpp

commit 3558af37437c88f32ebe44c8366afd2926b64f68
Author: almgren <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 8d417c07314914883564d2b87482739391b65aeb
Author: lijewski <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 00d1c148aabcc444e861e3adbe1fef3c5c4699c0
Author: lijewski <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 e4269273d2730588845f4849968fc5d2abc63e01
Author: lijewski <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 4e73babda294e50badb632f85a81feb0fdeef032
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:33:28 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 3b9e64b7934bb12991b634015bb0bae0473c7d2b
Author: lijewski <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 df1f332c6c71d3cfed5b19db251d7ce7567a2e25
Author: lijewski <lijewski>
Date:   Wed Jun 2 02:00:01 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/mg.f90

commit 663b4d64cc66702c11071aee6bf51c8160288f4a
Author: lijewski <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 9cc92b3ac37828934a5c9f7dc4f9c3e6eacc3bef
Author: lijewski <lijewski>
Date:   Wed Jun 2 01:25:23 2010 +0000

    removed some unused variables

Src/LinearSolvers/F_MG/mg.f90

commit b4ee73f4b936cdcba69c7376d1327dfeb7f15f45
Author: ajnonaka <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 b5326cd6d5b9ae41ef33e4fe2f94296240819366
Author: vince <vince>
Date:   Tue Jun 1 21:50:06 2010 +0000

    paths for kiryu.

Tools/C_mk/Make.mpi

commit 64663863101ff8d4e4d6d19990394163e7ee1842
Author: almgren <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 a6f4f9a352e9ba62c82713d4d5debe4ec0c8e772
Author: almgren <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 6a5fcd1076844b5d3ac8318309774a8425742e79
Author: lijewski <lijewski>
Date:   Mon May 31 15:52:09 2010 +0000

    plugged memory leak

Src/F_BaseLib/cluster.f90

commit 1ff62e70a9ecdcce3df43f81cf5701635dd245be
Author: almgren <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 b34105aa870ac5e8f31e4228d396e0d5c43eb816
Author: almgren <almgren>
Date:   Mon May 31 03:29:16 2010 +0000

    Fix indentation.

Src/C_AMRLib/Amr.cpp

commit 0a5391988ee06710297528d28c742c105f40fbf1
Author: almgren <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 31509bab5e79bf45e611a2de677e50a8a9e82240
Author: lijewski <lijewski>
Date:   Fri May 28 23:39:28 2010 +0000

    removed some unused variables

Src/F_BaseLib/pingpong.f90

commit 82a3a29c319b0b7db85e76ca92ec996b100a8dc1
Author: lijewski <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 5b7436543d4a1f483308b7fe059c22c6b02d95cc
Author: lijewski <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 51921159917355c87068c505e44b9e58fe7e6b0f
Author: lijewski <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 5157143439e5b17503504e26f81b2a91e5b9f218
Author: lijewski <lijewski>
Date:   Thu May 27 22:16:30 2010 +0000

    bit more cleanup

Src/F_BaseLib/tag_boxes.f90

commit 88baa8c6b4e6000d6c04a33966e0506ab254339c
Author: lijewski <lijewski>
Date:   Thu May 27 22:15:02 2010 +0000

    got rid of some unused variables

Src/F_BaseLib/make_new_grids.f90

commit f6b0283e965ab4fa67b01e71c626927b26c636bf
Author: lijewski <lijewski>
Date:   Thu May 27 22:13:57 2010 +0000

    tagboxes_coarsen() appears to work

Src/F_BaseLib/tag_boxes.f90

commit 1303d9f95c7b91a828b758424600aea1e52427fc
Author: lijewski <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 c27db6107db6f74f699dbe666831b9c13a263ac6
Author: lijewski <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 b9635c7ae491506772786d34c191d8ac21e1ff97
Author: almgren <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 6fe7cdc7ea40722dc481ccc64efa7addd9aa2ba4
Author: almgren <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 e4347ff498330463db1dcab1eaf4a5b7e04ee6e4
Author: almgren <almgren>
Date:   Tue May 25 21:56:21 2010 +0000

    One more fix...

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 3891a1c5771511a29e246f164cd32ef2d7eb9c12
Author: almgren <almgren>
Date:   Tue May 25 21:47:45 2010 +0000

    Try again...

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 6481c0e9f5e7c01fd4aa25cd16b093e2e7f123ca
Author: almgren <almgren>
Date:   Tue May 25 21:39:24 2010 +0000

    Fix mistakes.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit bef1f55cb6f5a9f4f2cd0ba6fc183c85802324c0
Author: almgren <almgren>
Date:   Tue May 25 21:24:14 2010 +0000

    Allow different number of state variables.

Tools/C_util/Convergence/DiffSameDomainRefined.cpp

commit 389e92849287aa501a03e709889f10972891f7f3
Author: almgren <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 a836688e3445766c68ef3f866e860ef2d9c78b1f
Author: almgren <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 e935dc6397d9da5c01d08f62ab1af74809802989
Author: almgren <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 3adedce0907535a07bfd901346cb15ff3b86e672
Author: mzingale <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 8492d9b73ebff5b3b875b6796176fbaf7a009ea8
Author: mzingale <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 40138d4397676a59ccd060c3f15622e92c38d9d8
Author: mzingale <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 905fa7fada383c7d7f5e49950abfadc409d34f38
Author: almgren <almgren>
Date:   Fri May 21 22:36:02 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 6ff6bcbf2a542c2e3eb21b888024c85bc24925cc
Author: mzingale <mzingale>
Date:   Fri May 21 18:59:26 2010 +0000

    comment tweaks

Tools/F_scripts/make_build_info

commit c9400fb21ada46e1aa68eaec1f9e472d457c11c7
Author: mzingale <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 e89b30278c2564ebe38466d3bb4bf0648c71a308
Author: mzingale <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 f47822b93e8c04936300a51675fd84c9bfa5a60a
Author: mzingale <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 60d1d73ed74ca3061e27b2c96c068ecfb56e8a4a
Author: mzingale <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 0c3a9c66550da0653302a0bd066e684f060427ee
Author: ajnonaka <ajnonaka>
Date:   Mon May 17 22:46:49 2010 +0000

    OMP fix

Src/LinearSolvers/F_MG/itsol.f90

commit 8b6ffc976e1c1917bafbeee126e4676f9160bcd4
Author: almgren <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 b9900b99c5c4580dce9f07e4b2d9944671718c8a
Author: lijewski <lijewski>
Date:   Fri May 14 18:06:17 2010 +0000

    intel icc does not support -fltconsistency :-(

Tools/F_mk/GMakedefs.mak

commit ff5991d734bfa4da7990c127662635d431342278
Author: ajnonaka <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 9d7bc140ac30c9fc90cea68dec4ede2fc3e6c99f
Author: lijewski <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 85614c1bd95afbc89cab4f618d290912ea15db78
Author: lijewski <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 6a31a33ffbc7476450f08b6a81de5a49631df163
Author: lijewski <lijewski>
Date:   Wed May 12 22:16:08 2010 +0000

    not needed

Src/F_BaseLib/omp.f90
Src/F_BaseLib/omp_stubs.f90

commit e6eab8e8e663ae98ca87780f22ff66e76b42365c
Author: lijewski <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 ff1e390efa63517527184c717a018914640251ac
Author: lijewski <lijewski>
Date:   Wed May 12 20:48:04 2010 +0000

    removed some unused drek

Src/F_BaseLib/box.f90

commit 0ca63e7ac9abc027c1146c89c7c54ffcf1cb200a
Author: lijewski <lijewski>
Date:   Wed May 12 20:35:26 2010 +0000

    removed some unused drek

Src/F_BaseLib/boxarray.f90

commit e9783133d200cf09e73455d319942de677857c16
Author: almgren <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 88bfca30c3f7f9cdb014a425d1b0987a0ea09fc3
Author: lijewski <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 6ab993142d35547d23e3b658d8b0903c99d0200f
Author: lijewski <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 7cc7035340912d28630f01c005b67eefbb0cafd8
Author: almgren <almgren>
Date:   Tue May 11 02:16:20 2010 +0000

    Fix comment for subroutine mg_defect.

Src/LinearSolvers/F_MG/mg.f90

commit a4d4ab7c403cb81fee9e1373e0c769c490091242
Author: marc <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 db159d88b0b393b44e734d8e4ab40b9e2b1423bb
Author: almgren <almgren>
Date:   Fri May 7 20:44:26 2010 +0000

    Add one line of comment...

Src/LinearSolvers/F_MG/mg.f90

commit f87d7687708257587b1a1c8d08d96d4c4645ce55
Author: almgren <almgren>
Date:   Fri May 7 20:13:52 2010 +0000

    Fix print statement for convergence.

Src/LinearSolvers/F_MG/ml_nd.f90

commit da65fb108b874aaf7656085afef4954fcac79ec4
Author: almgren <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 1d6f668dc4d9bb9111592d851aa01dbb2b28f201
Author: lijewski <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 db210dd0fea8f5c5449c2f6ac6aea3931dedc8dc
Author: almgren <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 98ddefae1107de7327802602b58af98990d372ca
Author: almgren <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 ad491ac2dca8758da04a2977d7ee4e80ac899b73
Author: almgren <almgren>
Date:   Thu May 6 01:58:28 2010 +0000

    Fix definitions of hi.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 718f2242b73ed75e738dd97ad31e0caa278c0a71
Author: almgren <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 73da9f4d113c57b1807de90277f95681328fb573
Author: almgren <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 6aa733f0e8fc88a9424160b5171162eab67753be
Author: almgren <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 e80ff5f49e3784dbb07f946cb93385dd90a8e896
Author: almgren <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 6ffda162a89528d3af78672fc2d26475e2c2c7e0
Author: almgren <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 dc1ffc3fc1fcf4692800d938f04d509feb6fb1ea
Author: lijewski <lijewski>
Date:   Wed May 5 20:17:25 2010 +0000

    got rid of some duplicate printing

Src/C_AMRLib/Amr.cpp

commit 1ebe07179051b43db9e06894dba23e133e618fa7
Author: almgren <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 bd8620391db49c1a1c5c3018ad4cb8662e8a87a2
Author: almgren <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 ec77f8c0aef19751a5d6ef9d9e8320c2be9e5aad
Author: almgren <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 573bd96fed8b17f25c1b4b330f2679ff687470f1
Author: almgren <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 3a270c1f12becf79b820759f6fcd960258c3111a
Author: almgren <almgren>
Date:   Fri Apr 30 17:37:01 2010 +0000

    Remove unused mg_tower_v_cycle_c.

Src/LinearSolvers/F_MG/mg.f90

commit 597ca62c813a03909a16b3497c7e9b85e78294f6
Author: almgren <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 aa0feb07d44fd697aba396474d71ee586edef571
Author: mzingale <mzingale>
Date:   Fri Apr 30 15:05:03 2010 +0000

    no, really add inf...

Tools/F_mk/GMakeMPI.mak

commit 05b66078785e39acb96df6d5393c9d87378e8e95
Author: mzingale <mzingale>
Date:   Fri Apr 30 15:03:55 2010 +0000

    add inf

Tools/F_mk/GMakeMPI.mak

commit 38ef8c0b3ce66aa09efce9e46d9af511ed377e76
Author: almgren <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 d0d9f705b0330e8249c3b47d762b460b76a11706
Author: almgren <almgren>
Date:   Thu Apr 29 21:34:40 2010 +0000

    Fix typo in previous commit.

Src/LinearSolvers/F_MG/itsol.f90

commit 50141672457b477c5eebc5aa614dd6332eba333d
Author: almgren <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 b9e83ed44529e7c390d86fc246811ecc9395af16
Author: almgren <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 c5e962c58aee068f18aad2054ef66a96ed3a0f4c
Author: almgren <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 c0cc9aaf2fd75ac278fc2ef5c00e35809b18bca0
Author: almgren <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 45d2630351325e05c8939c99aab304e7a894fba5
Author: almgren <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 79b611370d69a9949091d01148cb517fe6db6e58
Author: mzingale <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 0c1fafe604cb3f9c7febcbfe1d19133bb0dd308f
Author: almgren <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 5700c2ff886ac245976e8a02922584ed3e15b32d
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:57:29 2010 +0000

    now testing the new email list...

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 5c535b07abd01df0665c854b056168f2aa50e724
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:53:36 2010 +0000

    FINAL TEST COMMIT

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 4cfcded2a154c574740858e78a77480541111799
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:52:00 2010 +0000

    TEST COMMIT 3

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 11776e6fc079d7e8c67ba653fddfc347b33cd2ae
Author: ajnonaka <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 e566bec070944aaff2c9247753d00f48c1c08345
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:46:45 2010 +0000

    TEST COMMIT

Src/LinearSolvers/F_MG/stencil.f90

commit 42b0c154321936ffabb96bbbafd86ad3a2c1cc2a
Author: ajnonaka <ajnonaka>
Date:   Wed Apr 28 13:40:49 2010 +0000

    commit to test log messages - no changes

Src/LinearSolvers/F_MG/stencil.f90

commit 2fcb4844c3c3490c77e426a7da565eb612f0484c
Author: almgren <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 6db052890e275670d5ebd9aeffb8f0f0b215029d
Author: lijewski <lijewski>
Date:   Tue Apr 27 23:01:54 2010 +0000

    plugged memory leaks in bottom_solver==4

Src/LinearSolvers/F_MG/mg.f90

commit 240b53a5ca4990d34605ffbf935e4fd8eb87f10c
Author: mzingale <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 8e7668d7f1563612a21d4512099b99928908ce5a
Author: almgren <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 fc755c030a5b6e22193a78ef03f32bcf537a9243
Author: gpau <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 4b1fa65b01d115b904e96c4addf29b443b6ad0d7
Author: almgren <almgren>
Date:   Mon Apr 26 19:10:26 2010 +0000

    This version compiles...

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 770ea54542113050cb493ad3901a3ae6d4faca36
Author: almgren <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 b2e1b2cc9c0ac40f5f07d337ccfd5855d5c1bf9b
Author: almgren <almgren>
Date:   Mon Apr 26 17:23:07 2010 +0000

    st_coeffs --> coarsen_coeffs

Src/LinearSolvers/F_MG/FParallelMG.mak

commit c2225fa88c66ee77ecfdf90c56251638ebd0dd79
Author: almgren <almgren>
Date:   Mon Apr 26 17:21:55 2010 +0000

    edge_coeffs should be (:,:), not (:)

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b048ac5b7f3a1cbd983cf567c25228b76db0a1a9
Author: mzingale <mzingale>
Date:   Sat Apr 24 13:42:12 2010 +0000

    line wrap error

Src/LinearSolvers/F_MG/stencil.f90

commit abc0cf7c9dbb0afe1e22fce0c0dff0045feef1f8
Author: almgren <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 ef2e139c58074bbf0c4cd5a207b15aadaa34dd4e
Author: almgren <almgren>
Date:   Sat Apr 24 01:34:49 2010 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit 743960500674bb382f8ac274a4e6b85e0aa4ca26
Author: almgren <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 3134128407204972e679aa9879ddcf31f0d0680e
Author: almgren <almgren>
Date:   Sat Apr 24 01:08:53 2010 +0000

    Remove unused "cross" in extrap_1d.

Src/LinearSolvers/F_MG/stencil.f90

commit 0e2d47eed7088a3c011f6934bf85263e8f999b6b
Author: almgren <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 76aa67eaaf0d1760509a23e3429c89fc6611635f
Author: almgren <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 41596394aa92f7ca42cec06004f74ddd03b51480
Author: almgren <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 7e2022f022e94dff1895d497e24a7838def61ebf
Author: almgren <almgren>
Date:   Sat Apr 24 00:07:01 2010 +0000

    Typo ex --> dx

Src/F_BaseLib/tag_boxes.f90

commit c48f309a3739cb0176baa7973d79bcce8e9b1fe0
Author: ajnonaka <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 10909bb536dced456dad7833240c851903a1351d
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 23 22:36:32 2010 +0000

    rewritten in gfortran-friendly way

Src/F_BaseLib/layout.f90

commit fdd9cdc6fc1d3e5369d9640c997078ab4d8f53c4
Author: ajnonaka <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 8d74bfa9a7c16b813acf43867b825649fe791330
Author: almgren <almgren>
Date:   Fri Apr 23 21:34:20 2010 +0000

    Add multifab_build_edge routine.

Src/F_BaseLib/multifab.f90

commit 0f7a102cbc5cb1b1156d7363d94d4947ae1a43f3
Author: lijewski <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 708db30edc69bc870a57f4596b58dfd0922a9641
Author: almgren <almgren>
Date:   Fri Apr 23 18:33:18 2010 +0000

    Renamed st_coeffs.f90 --> coarsen_coeffs.f90

Src/LinearSolvers/F_MG/GPackage.mak

commit 2e3300b437f0a1782b3093bbecbfb034ce1975a8
Author: almgren <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 7bf63d38e64312fb77e68c2bbaf87ff7907a705d
Author: almgren <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 035f2fa353bcd9dd2d6fe1d0336049b82d872386
Author: almgren <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 6d75c2b01649cb6dfa97aba6f66915ef8b514866
Author: mzingale <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 eb0a3eb7cec65d2d713f35ca9fccbcef7ab1f515
Author: gilet <gilet>
Date:   Wed Apr 21 16:30:17 2010 +0000

    added stuff for orga

Tools/F_mk/GMakeMPI.mak

commit 4df043d6ddbfa92e0c2cf49586632ab978b6047d
Author: almgren <almgren>
Date:   Wed Apr 21 04:00:44 2010 +0000

    Pass in bottom_solver

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 175dc9fd7675ced09f7da3d9c44f09cbe53a3c11
Author: almgren <almgren>
Date:   Wed Apr 21 03:58:56 2010 +0000

    Fix a buggy part.

Src/LinearSolvers/F_MG/stencil_fill.f90

commit cae732c2e5d86a48da6498c39604ca1fcc593eaa
Author: almgren <almgren>
Date:   Wed Apr 21 03:57:48 2010 +0000

    Remove unused statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 70c32e7022b07cfcadda7805f04a812732051ea3
Author: ajnonaka <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 a741b73a1f3a45878cfd4478fd38e7f0bb1c3da5
Author: almgren <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 aaa81902be8a8bc539efed6a336764964a42f31f
Author: almgren <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 fff7307b7146bf03375df55d697c2398fbd2ddf6
Author: almgren <almgren>
Date:   Tue Apr 20 21:29:35 2010 +0000

    Fix interface for porous...

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 9841c4bc2fdd06a51ffeb49b4504fd2cac5d7bde
Author: almgren <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 c7e20ca1e3c792e66fa8b4091e3afad6c5469d62
Author: almgren <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 e156879ea1ca232cdda97c4afb43629c38665fdd
Author: almgren <almgren>
Date:   Tue Apr 20 20:34:37 2010 +0000

    Also need to include stencil_fill.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 58535e160a8a695098f4aae0cc657bc2b3220896
Author: almgren <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 ec4bbdd2e5ac334a4a2ea21064a32cb7ebcd4272
Author: almgren <almgren>
Date:   Tue Apr 20 20:31:06 2010 +0000

    Fix line 157.

Src/LinearSolvers/F_MG/mg.f90

commit 91dadbf8400d4440a1d35992ed35f3f3b8dd63b0
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 20:22:34 2010 +0000

    forgot to include impose_neumann_bcs.f90

Src/LinearSolvers/F_MG/FParallelMG.mak

commit a27d111b2b14b4756bf9bbcbdb026b3ec31cbd97
Author: almgren <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 4a034f087266ce8d9c0e222e2dc38bb4302f7052
Author: ajnonaka <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 7df24f54f9218376c3b0ed6388adfb004df475eb
Author: ajnonaka <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 69a9121bef43873beb31ccb055657935ac6b38c9
Author: ajnonaka <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 155b277949c13bc3f15ab8df107bf3d1bac9661b
Author: almgren <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 46571fceab7721ccc02f55b88463b762971c997e
Author: almgren <almgren>
Date:   Tue Apr 20 18:59:55 2010 +0000

    Added some new files.

Src/LinearSolvers/F_MG/GPackage.mak

commit c1efe4714b655f81f640eb5df3301892a7301525
Author: almgren <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 d3fda8b0f2db34149960fcbf6dc3a5acc11fcdc6
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 20 16:42:16 2010 +0000

    added some non-mpi support for interpid

Tools/C_mk/Make.Linux

commit 21004c6543d572fda8dac53cd75924509f0bcdf1
Author: ajnonaka <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 f2ff5a30b42121e93557b38428a648a04b96a22e
Author: lijewski <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 99c46dae8b76641c4c4f15ad6b01627e99f69bef
Author: almgren <almgren>
Date:   Sun Apr 18 18:35:05 2010 +0000

    Fix spelling of error message -- incommesurate --> incommensurate

Src/F_BaseLib/layout.f90

commit 74e09495507e129c690b462511a9c96cd38065b4
Author: almgren <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 f272db3466641e10a5a45b543e9fac4706ffdcea
Author: gpau <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 8628ab502af144d7bbbdd2249dfbb8b2bbb8a7f8
Author: gpau <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 1f71be283b763891190b8c5af1a968a765252507
Author: lijewski <lijewski>
Date:   Thu Apr 15 21:17:10 2010 +0000

    carver.nersc.gov stuff

Tools/F_mk/GMakeMPI.mak

commit e77850990aa0ace1af2ae32311a2c31f4fd575f2
Author: lijewski <lijewski>
Date:   Thu Apr 15 21:16:38 2010 +0000

    more junk for carver.nersc.gov

Tools/C_mk/Make.Linux

commit 7e6590ce8fd3a06da8bd05b2929ecb909e0e3b19
Author: lijewski <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 349668a1cfb882d4e282e73753c74c4b3e1b7e06
Author: lijewski <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 2ac678f346944cdbee7fec3905f0ea31c9b99c57
Author: lijewski <lijewski>
Date:   Tue Apr 13 23:14:54 2010 +0000

    added extern/random stuff

Tests/LinearSolvers/F_MG/GNUmakefile

commit 962c8b3c09833846f173b8f3860337cae2f4545e
Author: almgren <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 5ccc3bd361ef22edab88c64e9be75621f1ab51b5
Author: adonev <adonev>
Date:   Fri Apr 9 22:15:57 2010 +0000

    stochastic_varden now compiles OK

Src/F_BaseLib/GPackage.mak

commit 0b2323ee9871fdf6a8c7122e47889f78734e6800
Author: ajnonaka <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 3670809b263e39227e627ac5a103576fe925967d
Author: vince <vince>
Date:   Tue Apr 6 20:48:05 2010 +0000

    fixed default MPI_HOME.

Tools/C_mk/Make.mpi

commit b89f03e249032f371b575f51ac4dc0e12c1baa4f
Author: ajnonaka <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 f73d0058ef86c54c901b5ff0960ebb2153904bb1
Author: ajnonaka <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 fae1830465684d8f992a4185ded246e561ef74c6
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 6 19:45:36 2010 +0000

    OMP flags for xlf compiler on intrepid

Tools/F_mk/GMakedefs.mak

commit 4981ff8b0363b4eaeee2418e84f1abc7a1a6b0d9
Author: almgren <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 f09321eabc8f7b35f0a59efd89eddc0f0734edba
Author: almgren <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 55126f8bb31bf47ad7830d4024341119f0ada4f4
Author: almgren <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 154ea1427237fd7cfa60812dea23fec41de45213
Author: almgren <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 2b98a31669db89dfcfc3da9161bb9626028840b8
Author: lijewski <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 78332347574e76468d5354c1227b9f065691192f
Author: almgren <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 4cef706b6f47209138f8b21ab9878dd8382ae561
Author: almgren <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 8b32a3b9e5b15de906773768ab9727c9003d31bd
Author: lijewski <lijewski>
Date:   Fri Mar 26 20:33:02 2010 +0000

    fixed parallel bug

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 055f7e71ecf5ba8dc1898710e0a0b9a83b4b6ae3
Author: almgren <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 58a0dec142983c4598104f3efe73a5dbba039569
Author: lijewski <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 b4ec1a1244d52a33409761d34fc19fed17307671
Author: gpau <gpau>
Date:   Wed Mar 24 23:53:44 2010 +0000

    fixed an error with the pressure solve

Src/LinearSolvers/F_MG/stencil.f90

commit 851a2987446b3fd67a88f39b0aa20810592b6eed
Author: gpau <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 def0d12a075b69351564e36d22935a442e0c0b69
Author: gpau <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 110da6e43b7a9f84e9cb074daf3a5cc765ed7089
Author: lijewski <lijewski>
Date:   Tue Mar 23 19:17:33 2010 +0000

    hmmmm

Src/C_BaseLib/BoxList.cpp

commit b29a994fb50711afd040d08a11efcea5bf0d5fb7
Author: gpau <gpau>
Date:   Tue Mar 23 19:10:35 2010 +0000

    removed bad BL_ASSERT()

Src/C_BaseLib/BoxList.cpp

commit 498f6e5344284af087b12c824021fab3c2381c7f
Author: mzingale <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 25331b056d1c00f4bfdebb746a7ae30aabc54115
Author: mzingale <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 180683da6704811f314b1eb4395e24849cc59705
Author: ajnonaka <ajnonaka>
Date:   Fri Mar 19 19:23:06 2010 +0000

    mods for PGI and jaguar

Tools/C_mk/Make.Linux

commit c3427103935a87c179729aaf590b28dcc5a1f551
Author: gpau <gpau>
Date:   Fri Mar 19 18:05:17 2010 +0000

    fixed a bug in the simplen_2d

Src/LinearSolvers/F_MG/stencil.f90

commit b9b445573d6f8721535996b1d218696b5c4b7435
Author: mzingale <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 f9d8185836e15ffc5785dc9c990e6c0fc334d6a1
Author: almgren <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 56f12bed53bd0c00d27784acc5797e656bcc7fb8
Author: almgren <almgren>
Date:   Thu Mar 18 21:14:42 2010 +0000

    Fixing spacing in print statements.

Src/LinearSolvers/F_MG/mg.f90

commit 7a9d0b8e315e9abca86a447fc337eb3b478a00de
Author: almgren <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 93e98918e9212f2e882785a3b6c260a048d80cc9
Author: almgren <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 b682ebbfb7a4e210edfd93c2faa0081dde262d77
Author: almgren <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 7c75998374b1dcda9ec4230f5d0a9893034cc66b
Author: almgren <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 4cdd8418b299c3aac7e0979be78715df6bb829bd
Author: almgren <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 ceef10005eed532f61aa690afe0a8fac291c563a
Author: mzingale <mzingale>
Date:   Thu Mar 18 16:52:49 2010 +0000

    latest test suite

Tools/C_util/regtests/Maestro-tests.ini

commit 979375ae5ea84d6682cdb4efc42a217fe9c079f7
Author: mzingale <mzingale>
Date:   Thu Mar 18 16:52:14 2010 +0000

    pretty-up the output (now in color)

Tools/C_util/regtests/test.py

commit 8cd993b15429b2181cb8f6b7db915407d5312333
Author: almgren <almgren>
Date:   Tue Mar 16 23:44:51 2010 +0000

    Wrap BoxLib::Warning inside if IOProcessor test.

Src/C_AMRLib/Amr.cpp

commit e2a9b8e291fe012caf8647bdf8c8ef5d5e172910
Author: almgren <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 86e713a2b8c2ca65eee45e1bcc550cd8732dbef9
Author: almgren <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 f38692cac6fdb798edb83e9ac6d744b041caeb52
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 16 19:16:12 2010 +0000

    syntax fix

Src/LinearSolvers/F_MG/mg.f90

commit 35eac60a974a38332bb619b9c84da383b52d5a19
Author: almgren <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 b2e9db5ca467d128636ede135a7fe7fef1e9d14b
Author: lijewski <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 5a5f3177b1f3a4d6d85d0db24e71ccf828e332a7
Author: lijewski <lijewski>
Date:   Mon Mar 15 19:56:16 2010 +0000

    added levelCount()

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit fe05213485f2e2b12f85439cfed9a1260d9a3459
Author: lijewski <lijewski>
Date:   Mon Mar 15 01:15:22 2010 +0000

    added fredom stuff

Tools/C_mk/Make.Linux

commit 7825121247448df072727755ca2c6917b5128fab
Author: lijewski <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 72b98effe065706d613a6d17861263f8add6fa2e
Author: lijewski <lijewski>
Date:   Sun Mar 14 22:01:46 2010 +0000

    freedom added

Tools/C_mk/Make.defs

commit d8d601951081950fefaf2a5b0756e6f6bf03c91d
Author: lijewski <lijewski>
Date:   Sat Mar 13 01:24:22 2010 +0000

    OMP mods to compile with PGI

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit d971e7dce9b7a52aae8eb9b463abe4737096cf1d
Author: lijewski <lijewski>
Date:   Fri Mar 12 21:07:59 2010 +0000

    changed -O -> -fast for PGI

Tools/F_mk/GMakedefs.mak

commit c799b95142024ec5a08ffc6b9b60b5532b2629dc
Author: lijewski <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 51fbfa76709c0718edeeea630267a53a102e3c47
Author: mzingale <mzingale>
Date:   Thu Mar 11 03:38:22 2010 +0000

    fix a bug introduced during an optimization

Src/LinearSolvers/F_MG/stencil.f90

commit 9c37fd65388bec5250a2922b099b0c65cda24f93
Author: ajnonaka <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 fec5f80532389c3b7833b4c94622abe774bb6202
Author: almgren <almgren>
Date:   Tue Mar 9 18:23:25 2010 +0000

    Remove print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 79a9983eeef9131e70576705c4333cc96a4228cb
Author: lijewski <lijewski>
Date:   Tue Mar 9 17:01:01 2010 +0000

    fixed something I broke

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 1363325265f1b92ff020e408ffda578e410bc8c7
Author: lijewski <lijewski>
Date:   Mon Mar 8 19:02:52 2010 +0000

    *** empty log message ***

Tests/LinearSolvers/F_MG/nodal_multi.f90

commit 3224970e045b26f8f113613f939b79b369e464b7
Author: almgren <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 c0b139380c497694427c67df5f8878d79e28d3bd
Author: almgren <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 64ea68ac519687d7a1950824dc6cff7791143570
Author: almgren <almgren>
Date:   Sat Mar 6 04:25:35 2010 +0000

    Remove unused variables.

Src/F_BaseLib/multifab.f90

commit bb22403c674f9d2ee316a8e318320801d54adb1f
Author: lijewski <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 27ac6582b095c8f67ca9655079ff95786ed0e076
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:46:58 2010 +0000

    bit more OMP

Src/F_BaseLib/multifab.f90

commit 72909a6542987c16cdbf51ea8c174301ba2ff854
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:28:10 2010 +0000

    OMPd fab_setval_c()

Src/F_BaseLib/fab.f90

commit 34869373b82e62230e3f7405b9a0310e8ea8860b
Author: lijewski <lijewski>
Date:   Fri Mar 5 23:05:05 2010 +0000

    OMP'd norm_inf

Src/F_BaseLib/multifab.f90

commit b6427871074c9aab5514edc41060c91841671aa7
Author: lijewski <lijewski>
Date:   Fri Mar 5 21:52:58 2010 +0000

    more OMPing

Src/F_BaseLib/multifab.f90

commit 1354d5044558910d6e7a0afd92750000ab265a7d
Author: lijewski <lijewski>
Date:   Fri Mar 5 20:40:21 2010 +0000

    little code rearrangement

Src/LinearSolvers/F_MG/stencil.f90

commit ed5abbd35391fbefdcc1b1d5c9009d6408ba45e7
Author: lijewski <lijewski>
Date:   Fri Mar 5 18:58:48 2010 +0000

    some code consolidation

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit c3181a5fdde782df8bf0227c0310576cfc00d934
Author: lijewski <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 593f986ef8c21662fcf484365f68832777b706a8
Author: lijewski <lijewski>
Date:   Fri Mar 5 17:46:01 2010 +0000

    removed some duplicate code

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 0571aa1575b237485f052ffa8ec9a16c4fe604b2
Author: lijewski <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 f15bb8e950f96b076979680574bb167d4622c06f
Author: lijewski <lijewski>
Date:   Thu Mar 4 22:03:50 2010 +0000

    removed itsol_breakdown() -- not used

Src/LinearSolvers/F_MG/itsol.f90

commit 290e9e99b208a545808a5eaa19cd4a5122d2b6df
Author: lijewski <lijewski>
Date:   Thu Mar 4 22:00:53 2010 +0000

    some cleanup

Src/F_BaseLib/multifab.f90

commit d6efe30b2b0bd84f795e3721482d7c15e29df615
Author: lijewski <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 bfdb349e3e850e61bc03d3b927a8a3227bb42991
Author: lijewski <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 7d143ba543f5b1e309db7d937da8f7d2b7590230
Author: lijewski <lijewski>
Date:   Thu Mar 4 00:05:18 2010 +0000

    more eliding of function calls

Src/LinearSolvers/F_MG/nodal_mask.f90

commit 5007b56d3f7e04c43494991cbb800b6b5c0d84a5
Author: lijewski <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 f2d5c52fdd592fe0ec62553235dec04786b945c6
Author: lijewski <lijewski>
Date:   Wed Mar 3 23:17:39 2010 +0000

    some OMPing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit ce9d354acb2ff110ee7d169e5ca20df4e1ddc7fa
Author: lijewski <lijewski>
Date:   Wed Mar 3 23:13:07 2010 +0000

    OPM'd

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 4255b7c2e9a83d0cc3e19405246885f2974a2096
Author: lijewski <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 d00854ceb3c542114118c481f011c62fd6131154
Author: lijewski <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 498acd3bdfe8f3507f52a7d8a57c0ed64b8a4c9c
Author: lijewski <lijewski>
Date:   Wed Mar 3 18:11:03 2010 +0000

    OMP 7-point jacobi

Src/LinearSolvers/F_MG/mg_smoother.f90

commit a47c0f1e10d3958bc46b336dfdffcbccb8453497
Author: lijewski <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 58f8b84d7222e9e51bf20087f3426caaf3552f5d
Author: lijewski <lijewski>
Date:   Tue Mar 2 23:49:03 2010 +0000

    some OPMing

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 2d8f1aba27c5b2c9b35cf494152e13fdd8ab89b4
Author: lijewski <lijewski>
Date:   Tue Mar 2 23:20:41 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/mg_restriction.f90

commit c11a35cda09c9932706daf007876576f44edd5b2
Author: lijewski <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 3450c5650323ed8f34f8fbeac42f897115768d68
Author: lijewski <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 265a72ed327e5370d2d5bca6940665efa15eb2a2
Author: lijewski <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 7314f9e5e78ea5b00d7fdce15f49d82b9401821b
Author: lijewski <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 93e12e5587df3d17e374852db2c2d97ef39066df
Author: lijewski <lijewski>
Date:   Mon Mar 1 23:45:37 2010 +0000

    removed some OMP loops that crashed Intel

Src/F_BaseLib/multifab.f90

commit 9ed0c6758ff47af8a6a7f077d3c1bd13ca1d858a
Author: lijewski <lijewski>
Date:   Mon Mar 1 23:10:17 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit caee6b388fe9d5f4509f2db80aa843ea727efb52
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:43:58 2010 +0000

    yet more OMP

Src/LinearSolvers/F_MG/stencil.f90

commit 8b4ab52cbfcaa272dd2cdd28a237a5ff5076b7e9
Author: lijewski <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 693d83cd18376b1df263af1cf915c3a7999f30b7
Author: lijewski <lijewski>
Date:   Mon Mar 1 22:15:57 2010 +0000

    some OMP

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 72d94ddcbc6b2da968b9a4947fd526bf6cf5ee55
Author: lijewski <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 65cdb3dda7150b02fe6e4ce96a9fcabf6a90af17
Author: lijewski <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 272910eb9ad7dfdabc4a8b55c16f419ec65d2b85
Author: lijewski <lijewski>
Date:   Mon Mar 1 20:12:14 2010 +0000

    speedup to gs_rb_smoother_3d

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 594ddeb94343fc9862f3d251f6f34a8e8bbd54f5
Author: almgren <almgren>
Date:   Fri Feb 26 22:23:37 2010 +0000

    Remove unused variable:
    IntVect b1_length = b1.size();

Src/C_AMRLib/TagBox.cpp

commit 8adc964d67678a40e977cc5718c0dfd20784000a
Author: almgren <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 4f7467b63279338532a4d663db717cccf088d337
Author: lijewski <lijewski>
Date:   Fri Feb 26 21:33:58 2010 +0000

    minor efficiency tweaks

Src/C_BaseLib/BoxList.cpp

commit 09e955a8181919b798036d1d0ba068508013ca55
Author: lijewski <lijewski>
Date:   Fri Feb 26 21:14:00 2010 +0000

    minor tweaks to add()

Src/C_BaseLib/BoxDomain.cpp

commit e630d63e8164d7327e72230e6146fc96cd80b174
Author: lijewski <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 c3a0b5bc234fe1f45d411f2e810475062388bdd3
Author: lijewski <lijewski>
Date:   Thu Feb 25 20:59:23 2010 +0000

    undrrelxr now uses LnClassPtr instead of CpClassPtr

Src/LinearSolvers/C_CellMG/LinOp.H

commit 0a46529825fceb21e5246af37e6b616fd7c39bc6
Author: lijewski <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 ed5c1530ba0bedc52e46954792e5a665a9c4a34e
Author: lijewski <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 c974efeb44b9c18bfbbb63052719237a1e2cf92a
Author: lijewski <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 1cea6f82fc47ea06dee33a715df76fdfdf8402b7
Author: lijewski <lijewski>
Date:   Tue Feb 23 18:36:07 2010 +0000

    added swap()

Src/C_BaseLib/BaseFab.H

commit 6ebf9e8c60c12baa27b51fbb79c3dcf92ea2bcda
Author: almgren <almgren>
Date:   Mon Feb 22 00:53:12 2010 +0000

    Removed empty loop in Amr::restart

Src/C_AMRLib/Amr.cpp

commit e4032a3ba1397a618c39588087c16320a5870e9f
Author: lijewski <lijewski>
Date:   Sun Feb 21 16:28:19 2010 +0000

    efficiency mods to simplify()

Src/C_BaseLib/BoxList.cpp

commit 964ed5ff1f96d8931fdc03c19b7f59f4eb49b616
Author: almgren <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 9b443be98f48f14093ef75e77044d4f8198b9703
Author: ajnonaka <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 ed0babdcc7400e46294a14c542689bc206cf8c1d
Author: almgren <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 435415dde25c7f81ff5272dc3647091b2c78ade1
Author: almgren <almgren>
Date:   Fri Feb 19 22:44:51 2010 +0000

    Default COMP to Intel, not g++.

Tools/C_util/Convergence/GNUmakefile

commit b21f6ecd95f1e9022ce18b7f2e3df1fd0e2f6020
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 19 22:36:05 2010 +0000

    compiles again

Tools/C_util/Convergence/DiffFab.cpp

commit 347345acf80e750e7d6c0eb545864fd1fdb2c83b
Author: lijewski <lijewski>
Date:   Fri Feb 19 21:19:34 2010 +0000

    minor refinement of execute()

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit ace11fa8dfc102aafe5dc538e6c81a8e85dafc7b
Author: lijewski <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 f3481fcf61853daf9277ac3211099dea9833be4d
Author: almgren <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 e4d889612f0ef233f3b84d53af13a2c70876bfda
Author: lijewski <lijewski>
Date:   Fri Feb 19 17:59:07 2010 +0000

    removed BFProxy stuff

Src/C_BaseLib/BaseFab.H

commit cc12d50e562296a720fbff95bb607cc5cebc544d
Author: almgren <almgren>
Date:   Thu Feb 18 17:49:08 2010 +0000

    Fix print statements.

Src/LinearSolvers/F_MG/mg.f90

commit 15953644e28d55c5ccda2fe086c12153bd45006b
Author: lijewski <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 24a7d4ed3b1655ba336f140e337399154918d43e
Author: lijewski <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 a421807911ab68cb5172b163e03e9a53d670ae98
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:15:50 2010 +0000

    remove some temporaries

Src/C_BaseLib/BoxList.cpp

commit e38413400a46fe354c5c64ab57e75964e17732f9
Author: lijewski <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 a64839b99d0c446f2d34bdc847a0af6d9fa47ee0
Author: lijewski <lijewski>
Date:   Tue Feb 16 18:07:00 2010 +0000

    fix for more const-correct BoxLib

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 056f9351cd0c0a0cc28648dec5d58cdf8dd76f03
Author: lijewski <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 cc08f66459ac2149d2fe78592a3d876ce365bd19
Author: lijewski <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 340516ee0d1071b969773d9e2cb37feaff960046
Author: lijewski <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 6ff343958c4ad2fea116c590c57f088dcd7d78e1
Author: lijewski <lijewski>
Date:   Tue Feb 16 17:42:46 2010 +0000

    *** empty log message ***

Src/C_AMRLib/Cluster.cpp

commit 39e82ffdd4a346ad1c989144fd505fdf7410ba0d
Author: lijewski <lijewski>
Date:   Sat Feb 13 23:06:18 2010 +0000

    added cg.cpp

Src/LinearSolvers/C_NodalMG/Make.package

commit 7c36b7b016363342b5a38b4f6e04732f7f7a7f83
Author: lijewski <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 40b35b26b0b66dd1b8a64b7ac5ea35c8c58dc90e
Author: almgren <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 a15a9e5a51dc392a168afc3258631c6bdccf7339
Author: almgren <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
Src/LinearSolvers/C_NodalMG/gt_breaks_27pt
Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt

commit 3a937963a8ad0c5b70bc3e5f09b88f101e8e93fc
Author: almgren <almgren>
Date:   Sat Feb 13 01:15:26 2010 +0000

    Moved 3d_4_level.grids to the tests directory.

Src/LinearSolvers/C_NodalMG/3d_4_level.grids
Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids
Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids

commit 6119c0b82851e1b06d9f5bd87f232cfb34ac5aca
Author: almgren <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
Src/LinearSolvers/C_NodalMG/files.2d
Src/LinearSolvers/C_NodalMG/files.3d
Tests/LinearSolvers/C_NodalMG/files.2d
Tests/LinearSolvers/C_NodalMG/files.3d

commit 44bdfe67a7c29541e76b4ff04c9c57f1eff7ad7f
Author: almgren <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
Src/LinearSolvers/C_NodalMG/inputs
Src/LinearSolvers/C_NodalMG/proj.cpp
Tests/LinearSolvers/C_NodalMG/inputs
Tests/LinearSolvers/C_NodalMG/proj.cpp

commit 464e294d149a4a29bbf0f3a0bbded1e598ce3f0d
Author: almgren <almgren>
Date:   Sat Feb 13 01:10:35 2010 +0000

    No clue what hgproj.pg was for.

Src/LinearSolvers/C_NodalMG/hgproj.pg

commit 777e12089e0ed7952dfe4f39b83ed311db137fc9
Author: almgren <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 50e45ac8c85160bd272eba3e16a5f2402da2d701
Author: almgren <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 d91b862ab1933719b8282a45c4c5abe75adcc7a0
Author: almgren <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 f724e396c3504cfe31fe3d278e9c46c78f63f84f
Author: almgren <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 47e6d409d6d77a6abec8a90cd92335f42a29356f
Author: almgren <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 f6a8aeb898047f4dc47d0f99fbebc5ec02a30319
Author: almgren <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 56f97bc7c32d3733513dda6b39a34018dd548f75
Author: lijewski <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 fa7854bc451422f4b46417955d501fc4883785d2
Author: lijewski <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 fe34d39f9d2955c293c04e14701d40c19e8dc625
Author: lijewski <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 f868b912c916c78e77c6f79458a590256bb49a2b
Author: almgren <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 86c1e5d390cf07794def26da845d77475b323079
Author: almgren <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 09de753af5ac1e79b03bc3400f61ce56597728c7
Author: lijewski <lijewski>
Date:   Wed Feb 10 21:22:23 2010 +0000

    some refinement to Distribute()

Src/C_BaseLib/DistributionMapping.cpp

commit 46544a5792251f35ca6cbac9904fe8aa19e71976
Author: almgren <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 39a765832f5f0c8c63f3edcd7fc38df78474a993
Author: almgren <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 d0af494542496d85b579875fefda27dceebc2b52
Author: almgren <almgren>
Date:   Wed Feb 10 20:31:43 2010 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit d220743937059824e8ccb4f66a1582528fbeab9a
Author: lijewski <lijewski>
Date:   Wed Feb 10 17:32:03 2010 +0000

    some simplification

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit e34a8a101648187a7f9b3548d2f1051fc5b8214f
Author: lijewski <lijewski>
Date:   Tue Feb 9 23:04:49 2010 +0000

    added <cstdio> to get sprintf()

Src/C_BoundaryLib/BndryRegister.cpp

commit cfb8d82c00b3f5504647dc31fc5ed69905bbc802
Author: lijewski <lijewski>
Date:   Tue Feb 9 22:15:36 2010 +0000

    shut up some compiler warnings on franklin

Src/C_AMRLib/FluxRegister.cpp

commit ac440e9c0217474fe16ef8459288a1dc76bac39a
Author: aaspden <aaspden>
Date:   Tue Feb 9 21:00:42 2010 +0000

    Hopper

Tools/F_mk/GMakeMPI.mak

commit 1eb07ad3ba3512bf492dc327e4b753b90b734d56
Author: lijewski <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 9340f95aab244c8641204dd728ccb69cf8e8ccd2
Author: lijewski <lijewski>
Date:   Tue Feb 9 18:22:09 2010 +0000

    removed unused BL_ASSERT()

Src/C_AMRLib/TagBox.cpp

commit d8f3bc089f4615a5b19c70aba7f095f4bce5913a
Author: lijewski <lijewski>
Date:   Tue Feb 9 18:19:35 2010 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit 3106bcabd7dd5a5c0fedce275992b1b6f98968d5
Author: lijewski <lijewski>
Date:   Tue Feb 9 17:33:59 2010 +0000

    added some reserve() calls

Src/C_BoundaryLib/FabSet.cpp

commit 45c4b9434da0caf5724c47bcee6e2ae6222a83bb
Author: lijewski <lijewski>
Date:   Tue Feb 9 17:32:44 2010 +0000

    added reserve() call in intersections code

Src/C_BaseLib/BoxArray.cpp

commit e48a8802656f2a8dea7b2b62620d90b656a1f307
Author: lijewski <lijewski>
Date:   Tue Feb 9 06:32:27 2010 +0000

    some memory consolidation

Src/C_AMRLib/TagBox.cpp

commit 051acd89638951ebf07bd5ddfa19f9c9c2c33ec1
Author: lijewski <lijewski>
Date:   Tue Feb 9 06:05:55 2010 +0000

    use vector::reserve()

Src/LinearSolvers/C_NodalMG/interface.cpp

commit c53a5fbdd9ddc795731426fdb48a0d529579e7a6
Author: lijewski <lijewski>
Date:   Tue Feb 9 03:59:25 2010 +0000

    removed unused function

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 45d9daa80be0666d52d67b336c99fa1d9cb081a8
Author: lijewski <lijewski>
Date:   Tue Feb 9 01:08:39 2010 +0000

    now use vector::reserve()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 0c7787c2a19adda9c443cbcbe1f8982fe427c734
Author: lijewski <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 d593ca08223433cdc50dea3816103e57f9f0a9c9
Author: lijewski <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 bbefcdb2432a95d1f72301dfbef81a3277b10443
Author: lijewski <lijewski>
Date:   Mon Feb 8 23:39:13 2010 +0000

    some simplification

Src/C_BaseLib/BoxList.cpp

commit 4822ae757387222f0650f98857ddabd0a4e894fb
Author: lijewski <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 a0fbf90744d567e1cff56c630a5598f6f3d77654
Author: almgren <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 e9288e69e1df6ae1db33cedb675d5367d5997931
Author: ajnonaka <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 8a816da077f5f22157eb6ffd010b5e51e266f5a7
Author: ajnonaka <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 5e306a4b55a89ba4419c89d872d23c4e906b7b06
Author: ajnonaka <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 da21a61d985e93f23859ed33a357b273bcfd7005
Author: ajnonaka <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 2efe084620abf0967fb4a4b04423b1fead9e75cd
Author: ajnonaka <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 d0a24f67f32ba9014becb0e3d5d0b02241abc469
Author: lijewski <lijewski>
Date:   Fri Jan 29 21:14:02 2010 +0000

    additional optimization options for PathScale

Tools/C_mk/Make.Linux

commit 94efa1030dfffefcf27927e7e65c6ea86f06ee84
Author: lijewski <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 7a610c6a4c61a5841ff8390e41b895c975afc519
Author: mzingale <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 af5bcacd09de476fcfb40bdb874d5921d53ad2f5
Author: nazgul <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 c7ebd0d658469c3165e6f76a09ce5b31d920461b
Author: nazgul <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 33d1c3627bd4b68f7a3a6eff2a1aa0c482be928e
Author: almgren <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 16a220e3da70cc0920d6180d5386ae247463c629
Author: almgren <almgren>
Date:   Tue Jan 12 20:34:42 2010 +0000

    Fix print statement.

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit 37ffa94f372661f2cd5bac5a69af8f17e36c2c70
Author: gilet <gilet>
Date:   Wed Jan 6 01:11:50 2010 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 876b1799e1e2e8a9a1408581cef80a6e710af0f8
Author: lijewski <lijewski>
Date:   Wed Dec 23 04:34:56 2009 +0000

    disabled (again) FAST optimization for PathScale

Tools/C_mk/Make.Linux

commit 54d99ccfdcc749c40a4384e26ffe33d93d2ac889
Author: gpau <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 18565fd2328d91591044e9769375be4efee2f16a
Author: gpau <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 256919c2f6a0311f6732770d70686dcdaa7296a9
Author: lijewski <lijewski>
Date:   Mon Dec 21 20:36:20 2009 +0000

    removed stdnormal_cdf()

Src/C_BaseLib/Utility.cpp

commit 0d05884ad2edc7a726da5deeed5da5cc08b46226
Author: lijewski <lijewski>
Date:   Mon Dec 21 20:36:04 2009 +0000

    removed Output_CPU_Comm_Costs()

Src/C_BaseLib/DistributionMapping.cpp

commit 9d6470f2e72b9c62f524197db6c5b52a4fd028cf
Author: almgren <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 8e242c70c04836489413732bedb97182e29e77af
Author: almgren <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 9886ad560753c60793775f1d1841b9eaf221faf8
Author: lijewski <lijewski>
Date:   Mon Dec 21 16:07:03 2009 +0000

    disable fast stuff for PGI -- breaks LLNS

Tools/C_mk/Make.Linux

commit 38c872f2965cc45b57f3b818355002bfa875b59b
Author: lijewski <lijewski>
Date:   Fri Dec 18 19:04:17 2009 +0000

    put back some of the not NOFAST stuff

Tools/C_mk/Make.Linux

commit f154b2d99d66339e8c56a26e386bf0b1faa0a397
Author: lijewski <lijewski>
Date:   Fri Dec 18 18:41:34 2009 +0000

    don't print MFRead::: stuff by default

Src/C_AMRLib/Amr.cpp

commit 49d492ccec990e36e5a9ab27379ab63483d7b9ff
Author: lijewski <lijewski>
Date:   Mon Dec 14 21:13:58 2009 +0000

    disable the MFRead:: output

Src/C_BaseLib/VisMF.cpp

commit 509117d07672038849d806166cd231e9c270318d
Author: lijewski <lijewski>
Date:   Fri Dec 11 03:05:08 2009 +0000

    some cleanup of InvNormDistBest()

Src/C_BaseLib/Utility.cpp

commit c95f9bb47fab0e23e1f2b0ab210e724e6318eb38
Author: lijewski <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 e05b1df5f526d9dca20eb0910c94564915588942
Author: vince <vince>
Date:   Thu Dec 10 22:49:30 2009 +0000

    added code for more file system friendly restarts.

Src/F_BaseLib/fabio.f90

commit a4a6f2bdacf3becf035e084221cc1f38dbc1c205
Author: almgren <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 7a270eb52b095b1d1604ff89d1edbfb12857f2de
Author: almgren <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 8f05eb45d616e9bc63b297bdeeb503c86b604185
Author: almgren <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 dbbdcc6b06df0398efadfb84090e7ce69c4dc3a5
Author: lijewski <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 6568e4b1ac4df44e6813892988520f2d1362497f
Author: lijewski <lijewski>
Date:   Wed Dec 9 06:37:50 2009 +0000

    modest speedup to mt19937 code

Src/C_BaseLib/Utility.cpp

commit f48a119138e5bf9c7e72287504c74f9afdc68be9
Author: lijewski <lijewski>
Date:   Tue Dec 8 22:36:42 2009 +0000

    increased a buffer size by a tad

Src/C_BaseLib/VisMF.cpp

commit 33a9a984a2763f8256235362ea77c4ba4220602c
Author: lijewski <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 861c8028272c21c98cf63d178e1051b79048d667
Author: lijewski <lijewski>
Date:   Tue Dec 8 19:23:14 2009 +0000

    added blinitrand() entry point

Src/C_BaseLib/Utility.cpp

commit 8f88b8002cdcbd0ed7f8049145b461d3a6fcc617
Author: almgren <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 eba5908d25a9510a948e7b00961a2a074250867a
Author: lijewski <lijewski>
Date:   Fri Dec 4 18:21:56 2009 +0000

    fixed bug I introduced yesterday

Src/C_BaseLib/Geometry.cpp

commit 2eb5c494c60c3d87d4897801171754e25b2b3774
Author: lijewski <lijewski>
Date:   Fri Dec 4 17:35:13 2009 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit ff6ed3e354fecc58610552b970300c18484d256f
Author: lijewski <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 1e2fd5d64b606b66d865f58aefe40f1f24112802
Author: mzingale <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 57aac64b6177b2e78e66d3d94d61f6db31167b54
Author: lijewski <lijewski>
Date:   Sat Nov 28 07:27:53 2009 +0000

    up rMAX to 16 from 8

Src/C_AMRLib/INTERP_3D.F

commit 1655a36f3facfeb48d2ab858364adeb7bbece521
Author: almgren <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 7d5b91b9f2bb99f5e5fb2245ddd5ba3060db9242
Author: minion <minion>
Date:   Sat Nov 28 00:23:19 2009 +0000

    fixed stencil

Src/LinearSolvers/F_MG/stencil.f90

commit 03a439e763265f448cc857469dec83d268fc1bd0
Author: minion <minion>
Date:   Wed Nov 25 18:14:11 2009 +0000

    var density mg still not working

Src/LinearSolvers/F_MG/stencil.f90

commit 9e589c07117ae2e6c44dbf1a90e909a78bba365e
Author: lijewski <lijewski>
Date:   Wed Nov 25 05:28:18 2009 +0000

    refine_grid_layout yet again defaults to true

Src/C_AMRLib/Amr.cpp

commit 1b2ac7c1e94630cd472767c073fbd0bbfecc15d5
Author: lijewski <lijewski>
Date:   Tue Nov 24 18:37:17 2009 +0000

    mods for hopper

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 760a59d52c3567037aaadd3101de6881e2e0751b
Author: lijewski <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 9fcdbad29cadde193636572aad40d19ac86c5397
Author: lijewski <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 ac51d30c86f049e38d09e3fda8dc482521436cf9
Author: lijewski <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 9331aa558eadec00f39f304bf018b0dae6ff2997
Author: lijewski <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 364dacedb114f3eaf02c06cb1c0dd579f359e7bc
Author: lijewski <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 2e6b7e4634451f0165f4f5f80f7ab78c7f1e6806
Author: lijewski <lijewski>
Date:   Tue Nov 17 22:14:46 2009 +0000

    yet more OpenMP

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit de6bf740e099634e7ef69ffb3645514378f924ea
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:52:53 2009 +0000

    yet more OpenMP

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 9c7df66a9d7715a66667d975131b51150bc7b096
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:40:58 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit f395a3f4a4cb39f379fde51c7f5f0d9e4553f62d
Author: lijewski <lijewski>
Date:   Tue Nov 17 21:19:20 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 8d49e1e3d87ff07e78ec73591150cd0d08662424
Author: lijewski <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 f396b90bd359a81b89013288ee734647aa4e0cc4
Author: mzingale <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 435c9668a172179a935d1487db5a670fa4351a14
Author: almgren <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 f2625d79d368a65c48897c6079e5b52895c0068b
Author: almgren <almgren>
Date:   Tue Nov 17 03:01:00 2009 +0000

    Add 1d version.

Src/LinearSolvers/F_MG/nodal_newu.f90

commit b2d134e97ffeac5622d8985120e3f425ed00313d
Author: gpau <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 877cf57ae28f595f9bc8d49df9fa1fc077803eb9
Author: gpau <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 bea7fcb556ca90d80781c18b2416d72629a98878
Author: gpau <gpau>
Date:   Sun Nov 15 00:06:43 2009 +0000

    update the outputfile

Tools/C_util/Statistics/PltFileStat.cpp

commit 374e8982126a26ec5d00cee47caff4989f5b316f
Author: almgren <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 9ad00e0b814dd5bd5b13a6bcac8d0dae77a57953
Author: almgren <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 7fe039c2c42c1c3c45c60fc9c47c2d6d10605e9b
Author: gpau <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 11b2a13bacb7814728c5fabdcc854e6d4acedc20
Author: gpau <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 85dae7c2e4c8b742f30d756d52c90517609536ff
Author: almgren <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 db3d42a8414898f93effb45aa6f3ffc271845abc
Author: almgren <almgren>
Date:   Wed Nov 11 22:19:52 2009 +0000

    Just a cleanup..

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit 4870a71bbab3efcced6242275c3d8cf33e66419e
Author: ajnonaka <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 e49932319029023d9ba58586488035732a64d359
Author: lijewski <lijewski>
Date:   Wed Nov 11 20:37:02 2009 +0000

    add -fpconstant to Intel fortran and some simplification

Tools/C_mk/Make.defs

commit 61fa4cdb85eb2ce5718e2166c4639a5e0a74c0a9
Author: lijewski <lijewski>
Date:   Wed Nov 11 20:20:36 2009 +0000

    decrease Intel optimization -O3 and -ip are buggy

Tools/C_mk/Make.defs

commit d3c57e86c849536a2223d526e88724d09c64d0d2
Author: gpau <gpau>
Date:   Tue Nov 10 23:26:05 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit 324bbef71c214ac92dc4f44a9f2505642676edd4
Author: gpau <gpau>
Date:   Tue Nov 10 22:19:48 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit 2d1ef1513d2ec82984d753740ece28d719595212
Author: lijewski <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 85d6a0a0e908d3ebee9842a3e55848249dbc3120
Author: lijewski <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 b47707c1c07f118ed34a490c037af97891e6b3c4
Author: gpau <gpau>
Date:   Tue Nov 10 21:39:32 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileList.cpp

commit a40abdeeb407fb51d308c39140f555f9fb912ce3
Author: gpau <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 b6d6ddc516c41502c7b86ca69bd8e33060de7734
Author: gpau <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 55f02c7787a2f8b5544cc87494e4cf70ec90f8fc
Author: nazgul <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 4516e1fed1a061c731eacff7118e947f487485da
Author: almgren <almgren>
Date:   Tue Nov 10 02:32:38 2009 +0000

    This version should now work with della.

Tools/C_mk/Make.mpi

commit b305edb12ec62e5e369e1d321430d9e6728ca881
Author: lijewski <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 7ee40342542d1b1877ecb9136d3dbb85e451941f
Author: lijewski <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 c4010da42028ee907df897d2dc76dd625d2ad1aa
Author: lijewski <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 3d5cbe79d90f8ac3ad76622ff80dd90b562b9750
Author: lijewski <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 7713c5484fc2b03b7182979ac3cbf9a6e8b5e4ca
Author: lijewski <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 4a86a09115e86b8ddf2061377b958a04af954851
Author: lijewski <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 6fcf7d2394c136e15d5e15eb1d45c0e84925652e
Author: lijewski <lijewski>
Date:   Fri Nov 6 20:06:43 2009 +0000

    replaced some usages of MFIter::fabbox()

Src/C_AMRLib/FluxRegister.cpp

commit 49bf957831f66508f4fd27f60cb7c471bd702a2a
Author: lijewski <lijewski>
Date:   Fri Nov 6 18:33:23 2009 +0000

    some cleanup

Src/C_BaseLib/FabArray.cpp

commit 197f3b44b7f0e9835f1d02d26d0b9427fa97fa7e
Author: lijewski <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 daeed7514d0b210059f9a810f3b850e8cd3e8beb
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:41:37 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/LP_3D.F

commit f9aefdd961aeafbf0b185bb407ebb79fe5c17c2e
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:34:18 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 3d06b1da3eac3e12e5040584d23567e0662dd361
Author: lijewski <lijewski>
Date:   Thu Nov 5 23:23:24 2009 +0000

    more OpenMP mumbo-jumbo

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 03b3ae382b794b41c7c1d2e12f27a79d04e6b6c5
Author: almgren <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 0820a0e3e5ca00d47059b3080caf7726a4559e93
Author: lijewski <lijewski>
Date:   Thu Nov 5 22:45:37 2009 +0000

    OpenMP'd

Src/C_BaseLib/COORDSYS_3D.F

commit 4b2605e0dc12206b0fadac139572e1e104fe765d
Author: lijewski <lijewski>
Date:   Thu Nov 5 22:33:23 2009 +0000

    OpenMPing FASTCOPY() is a lose

Src/C_BaseLib/SPECIALIZE_3D.F

commit e8cac118302d0cff051bb9de6d72b7325ead9c4d
Author: lijewski <lijewski>
Date:   Thu Nov 5 21:30:53 2009 +0000

    more OpenMPing

Src/C_BaseLib/SPECIALIZE_3D.F

commit eae53271303197c06c2b0e18e19b3e676396506c
Author: lijewski <lijewski>
Date:   Thu Nov 5 07:50:40 2009 +0000

    commented out one pragma omp that kills PathScale

Src/C_AMRLib/FluxRegister.cpp

commit 7e0a110f731bc73f12dd66818471d4acbbebc22f
Author: almgren <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 590893d22db433961ec1122063de0878a7622a39
Author: lijewski <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 6cc63ee482b409ad8dbfcfeec0a0568f854a24a6
Author: lijewski <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 a6be3f01aecc63cabab1f87d8ab0af4a62d4e43b
Author: lijewski <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 2f57b8e3739880e88ea8af4e1b98e4a41fa556e9
Author: lijewski <lijewski>
Date:   Wed Nov 4 17:11:39 2009 +0000

    now thread applyBC() across FABs

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 59158bd1c139c9b0dbad06d6dcc4e1891cb66b06
Author: lijewski <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 578dc85d4b467ca682b4c378e35651f7f2e73826
Author: lijewski <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 dd9d491d5033f5c039de6d5a7ad9d659455536c2
Author: lijewski <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 c2ace2dd5226a671fa0111ae2036adad6cc213ee
Author: lijewski <lijewski>
Date:   Tue Nov 3 21:37:29 2009 +0000

    more OpenMP stuff

Tools/C_mk/Make.defs

commit b7acbcb7a5d22eb33bbe6e9191fcc31323ceae7c
Author: lijewski <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 5bf4242e44b5e1160e8d833cdda5c3e4df558c37
Author: nazgul <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 9e20b0e8168117d6404d6a65edbf2b50ad7700d9
Author: almgren <almgren>
Date:   Wed Oct 28 20:18:31 2009 +0000

    Minor tweaks for 1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit c789df7bd7f873f69d8d423d6bbe0f20b95fca80
Author: mzingale <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 b56f2cf317fdf4fe714006f1241e9322f1c06bf3
Author: lijewski <lijewski>
Date:   Tue Oct 27 21:05:48 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 9a48bfff893f64c5502380328cea5fadacce0b98
Author: lijewski <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 f0d3555054aeec9f1f0c2233fa58010feb47a5fc
Author: lijewski <lijewski>
Date:   Tue Oct 27 20:06:01 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 602f7e441e1fe074dea29f1d11343d87b70498f9
Author: lijewski <lijewski>
Date:   Tue Oct 27 19:37:59 2009 +0000

    more OpenMPing

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 77125099a334565419fbda317792d6c41363ab83
Author: lijewski <lijewski>
Date:   Tue Oct 27 19:09:12 2009 +0000

    more OpenMPing

Src/C_AMRLib/FLUXREG_3D.F

commit c059664f9a0b8c42113483708e940bb906c3f99b
Author: lijewski <lijewski>
Date:   Tue Oct 27 04:55:45 2009 +0000

    some OpenMP

Src/LinearSolvers/C_NodalMG/hg_avg3d.f

commit 4c400148bd7882ead59d65a05f19858b40dd1678
Author: lijewski <lijewski>
Date:   Tue Oct 27 04:43:04 2009 +0000

    some OpenMPing

Src/C_AMRLib/FLUXREG_3D.F

commit c54a6c9a1b71a7a8315ea00a190601790549647e
Author: lijewski <lijewski>
Date:   Mon Oct 26 21:58:40 2009 +0000

    print out size as well as initialize() time

Src/C_AMRLib/AuxBoundaryData.cpp

commit f354024b21c990d59ef4a27682b656dbf1b02e51
Author: lijewski <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 e3493b274827c735f8d0943b970e48c822415bf5
Author: lijewski <lijewski>
Date:   Fri Oct 23 20:12:29 2009 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 9a4c2b086a3aa3e0110739e4cd3d3d89d599b534
Author: lijewski <lijewski>
Date:   Fri Oct 23 19:57:50 2009 +0000

    OpenMP mods for Intel 11

Tools/C_mk/Make.defs

commit ed62805ce598790acbbccddeb3711c8d59601196
Author: lijewski <lijewski>
Date:   Thu Oct 22 21:00:30 2009 +0000

    removed OpenMP directives from FORT_NBINTERP() - buggy

Src/C_AMRLib/INTERP_3D.F

commit 80be497c5f9db7a00560190473eb9178fe191c0a
Author: vince <vince>
Date:   Thu Oct 22 19:24:32 2009 +0000

    added the new mothra.

Tools/C_mk/Make.mpi

commit b468a81f49c76aea85821b331cec26a55032b400
Author: lijewski <lijewski>
Date:   Tue Oct 20 22:47:35 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit b7e414649466239df5fe23b83bdd9ae3cd7ff5de
Author: lijewski <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 4d74a9ef671f8c80ff9e049babfc9a46ddae40be
Author: lijewski <lijewski>
Date:   Fri Oct 16 18:17:21 2009 +0000

    OpenMP mods to quiet PathScale

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit af6008a486d35ee41584eda774a40786a96be269
Author: lijewski <lijewski>
Date:   Fri Oct 16 17:04:09 2009 +0000

    OpenMP tweaks to quiet PathScale

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit c1c3004e24ceb0a3da7f74f1a1e1b77eec69e20e
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:39 2009 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 69cfea3713ac21f1370f71c1f092a32941bcd1f9
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:21 2009 +0000

    Fix 1d version.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit d6efd48f83a94807127b0850ba4a90cd86c19cdd
Author: almgren <almgren>
Date:   Thu Oct 15 21:57:10 2009 +0000

    Add impose_neumann_bcs_1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit cf7cb67f0c1aa1414efab19f6c021e450d8039a2
Author: lijewski <lijewski>
Date:   Mon Oct 12 21:40:17 2009 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit b818bbcae55a86b7d41a9ce825e3d7566cdf0bed
Author: lijewski <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 c0ba4ef4d6a6174e876838af41f45f9e1db30b99
Author: mzingale <mzingale>
Date:   Sat Oct 10 20:54:02 2009 +0000

    add Intel 11, and support for atlas

Tools/F_mk/GMakedefs.mak

commit c329d49862f2d215078c8558dc7cea9ff51860e5
Author: gpau <gpau>
Date:   Thu Oct 8 22:50:52 2009 +0000

    removed a bug

Tools/C_util/Statistics/PltFileXAve.cpp

commit f6a92cd0ffb004c6419e2efc55e89600340c0d1b
Author: lijewski <lijewski>
Date:   Thu Oct 8 22:10:56 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 2e42b725677a4ee02bb731614616b3c368c1322b
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:50:46 2009 +0000

    more OpenMP

Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 6487fdcbb581665f6e44e4383cd3366077aa7ae7
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:38:47 2009 +0000

    more OpenMP stuff

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit bd7507f1e0b46f6d7845f329037e3e77c9f0a11e
Author: lijewski <lijewski>
Date:   Thu Oct 8 21:05:19 2009 +0000

    redo of OpenMP stuff

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit d12a610b24d59c691f97fdc2ec8db4a0898e8624
Author: lijewski <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 26ec22d710ee56f623adb55d24e8df550f08d1e7
Author: lijewski <lijewski>
Date:   Thu Oct 8 20:29:52 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 49e1c9ad0ce6bbc3ec4ae47fca03fb57b87e9433
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:58:43 2009 +0000

    mods to work with PGI OpenMP

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 88bd7f66b1358412f3d02d944a698410745bf6d7
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:41:02 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 1d20ebec2d9f87324950435d216fb70c423faae3
Author: lijewski <lijewski>
Date:   Thu Oct 8 17:40:47 2009 +0000

    more OpenMP

Src/LinearSolvers/C_TensorMG/DV_3D2.F

commit 65a4f8366a2562e36cbbcdcd361f65a94cb36c54
Author: lijewski <lijewski>
Date:   Wed Oct 7 22:14:01 2009 +0000

    more OpenMP directives

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 400946386ceeff68cea7e44a77fd41546a9aa9a0
Author: gpau <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 e989cc894374c4946acbc14d754b2e9d11362f4d
Author: lijewski <lijewski>
Date:   Wed Oct 7 21:19:17 2009 +0000

    more OpenMP junk

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit d49bb271bdb47758424f137745588f8068d3f90b
Author: lijewski <lijewski>
Date:   Wed Oct 7 21:00:43 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 6a3a04c57bca7110d4c48165527c82f3f44581ed
Author: lijewski <lijewski>
Date:   Wed Oct 7 20:24:37 2009 +0000

    more OpenMP directives

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit 18d38aec276197592e32041f7c3a0ae6c095fdc9
Author: lijewski <lijewski>
Date:   Wed Oct 7 18:06:04 2009 +0000

    added some d0's on constants

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit eb22a2f65149e29403b37f3371989930f1a7333c
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:58:54 2009 +0000

    added some d0's on constants

Src/LinearSolvers/C_TensorMG/DV_3D4.F

commit 26ba8674706868673a564315fd30bed3eb9816c9
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:58:29 2009 +0000

    little simplification

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 0fa95dc5ecaafec3c19b0bbb4d0504cae8d0adb7
Author: lijewski <lijewski>
Date:   Wed Oct 7 17:31:01 2009 +0000

    workaround for PGI OpenMP bug

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit f36e59b9c1ecebf4463749dfe77041d69249999e
Author: lijewski <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 cec6d0bed60de6b02e5f8952f6fa1b2580659955
Author: gpau <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 1bf20c60cf3a86f5d3279c38d67607865ce8c76c
Author: gpau <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 84dc30072f95acb23812addb4973e512c653ff3c
Author: lijewski <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 dcd51e6cb7c3dda6d67e8b1a888b67a04e2e73c3
Author: lijewski <lijewski>
Date:   Tue Oct 6 21:37:14 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D3.F

commit 88e66a141f673ea8f6968fcc0121c9f2eca23cfd
Author: lijewski <lijewski>
Date:   Tue Oct 6 20:30:16 2009 +0000

    added FORT_FASTONENORM() and FORT_FASTZERONORM()

Src/C_BaseLib/SPECIALIZE_1D.F

commit 566df3ba5c3d2125cfe9ffe344633eca4b11a104
Author: vince <vince>
Date:   Tue Oct 6 20:00:31 2009 +0000

    addend angilas support for mpi.

Tools/C_mk/Make.mpi

commit 0b35f673e04bdfe93a03e86a2501e706899f10a3
Author: lijewski <lijewski>
Date:   Tue Oct 6 16:02:18 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D2.F

commit e51320eb6ca4e7df0a91943daa42857ddf2a57a4
Author: lijewski <lijewski>
Date:   Mon Oct 5 22:49:21 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/DV_3D1.F

commit 7ee06f6c2044de46cfc7d1681fc737fafb290ef7
Author: almgren <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 79802855937cbbaa0a388b783ded7ed8b4647adb
Author: lijewski <lijewski>
Date:   Mon Oct 5 21:47:50 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit 0b3ded9d1c1b9fd4756cf4fb51b9e79164ef513f
Author: lijewski <lijewski>
Date:   Mon Oct 5 21:13:20 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_TensorMG/MCLO_3D.F

commit a39e4e29466c057114349e68404c8d7a0d506c3b
Author: lijewski <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 bdbb3f467f717b10305f9caace4408c5372211ee
Author: lijewski <lijewski>
Date:   Mon Oct 5 16:41:30 2009 +0000

    OpenMP'd hgints() hgrlxu() & hgresu()

Src/LinearSolvers/C_NodalMG/hg_multi3d.f

commit 89f68ff8b4fd1f836f1594a2064f4aa0400b5182
Author: gpau <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 8cf622a6824b5ff17fb946b6aae6c3cacfb03d18
Author: lijewski <lijewski>
Date:   Thu Oct 1 21:20:40 2009 +0000

    OpenMP'd node_bilinear_interp

Src/C_AMRLib/INTERP_3D.F

commit d37282849f1613bb84ad5b60dbf1b987cdd5bf2a
Author: lijewski <lijewski>
Date:   Thu Oct 1 20:51:08 2009 +0000

    *** empty log message ***

Src/C_AMRLib/INTERP_3D.F

commit 7c9397a8049800cce5d05c8dad07fac9a2a615b2
Author: lijewski <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 3213772f7601cbfa63f0c7a04e498745f3d10892
Author: lijewski <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 7e9bb2f108992965495776bc86522d165f8678a1
Author: lijewski <lijewski>
Date:   Tue Sep 29 20:42:36 2009 +0000

    removed WorkQueue stuff

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit e7a7e4c109fd860ad2358dd5190a11bb7fac25ba
Author: lijewski <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 86519b50dae37adcf345a47ae8eb20c51312b1df
Author: lijewski <lijewski>
Date:   Mon Sep 28 21:13:32 2009 +0000

    SELECT instead of IF

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 1fa4c98ffde609ff947680e9619ea4849932b9bc
Author: lijewski <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 253e28a65fa8445f7773a519651c922bf834b138
Author: lijewski <lijewski>
Date:   Mon Sep 28 20:29:59 2009 +0000

    use SELECT instead of IF

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 3cbcf32c539078289602b765394339b789b1d659
Author: lijewski <lijewski>
Date:   Mon Sep 28 20:14:48 2009 +0000

    some simplification of APPLYBC()

Src/LinearSolvers/C_CellMG/LO_3D.F

commit 48ab6df446a9a19174290f1952bfbd0e0828c899
Author: lijewski <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 5c2730e829110e4bd6132250783ad9950e532a45
Author: lijewski <lijewski>
Date:   Mon Sep 28 19:13:53 2009 +0000

    OpenMP'd

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit d6e105f05a0a47a9640ecbeec321a11fc30a80fb
Author: lijewski <lijewski>
Date:   Mon Sep 28 18:09:11 2009 +0000

    yet more OpenMP tweeking

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 4df2f04ef1c225e0a01535ba0c2e7627a1c06e5b
Author: lijewski <lijewski>
Date:   Mon Sep 28 17:57:54 2009 +0000

    more OpenMP tweeking

Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F

commit 6ecea4d686f385d4feb8b1f21894f4ab0ea65158
Author: lijewski <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 db127c7c113a2d65592b71179f870533319991f8
Author: nazgul <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 351ed7dcd1f70a56680095e09331d9e051d75a22
Author: lijewski <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 f2e82b1c253031bdcd97987c5bdb784bb5fe6dea
Author: lijewski <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 e409fda5a5fd4c50c375b4f8e654918fb6d1c3b5
Author: lijewski <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 88dd1854afdf2132f7c0075dc417b50307506190
Author: lijewski <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 a9bb3cae07fd5c80513da2613ca5c75b77af13ae
Author: lijewski <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 638640ae292cb3a55e99976559479da16eb22b42
Author: lijewski <lijewski>
Date:   Fri Sep 25 03:50:56 2009 +0000

    rearranged some OpenMP stuff

Src/C_AMRLib/INTERP_3D.F

commit ee4ff2b74444c7a5018786e6e6395b2a5241cba8
Author: lijewski <lijewski>
Date:   Thu Sep 24 21:48:47 2009 +0000

    added some OpenMP directives linccinterp

Src/C_AMRLib/INTERP_3D.F

commit 35c7ffba5f9146fdf547db31814472a99e0ed6cb
Author: lijewski <lijewski>
Date:   Wed Sep 23 21:59:07 2009 +0000

    some OMP stuff

Tools/C_mk/Make.Linux

commit b3d4c2cd6d2a805925ab7980727164931f01b3a4
Author: lijewski <lijewski>
Date:   Fri Sep 18 22:10:33 2009 +0000

    some OpenMP stuff

Tools/C_mk/Make.defs

commit 6f70f0283d1d9cb0c554413087927f3bd6aeb270
Author: ajnonaka <ajnonaka>
Date:   Fri Sep 11 23:26:57 2009 +0000

    OMP=t option for PGI on franklin

Tools/F_mk/GMakedefs.mak

commit d1c8a4ebaf3889aaf2620a46450e64733993b9f8
Author: vince <vince>
Date:   Fri Sep 11 18:20:09 2009 +0000

    more 11.1.

Tools/C_mk/Make.defs

commit 5e9da5df15e6bca7951e2d121099cf23b8086bcc
Author: vince <vince>
Date:   Fri Sep 11 18:13:19 2009 +0000

    intel 11.1.

Tools/C_mk/Make.defs

commit b4ec7e42dab71ce96418672243662f4a642c1d6d
Author: ajnonaka <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 d34ef67b4c3b9884a6e252a7b389b50103d7abb2
Author: lijewski <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 c047e8998f41a80842e8ff1b4dba819a4e08fba5
Author: mzingale <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 1f6187e4f4f041b4cfeadcecbba7b6e316db5a80
Author: lijewski <lijewski>
Date:   Fri Aug 28 16:55:31 2009 +0000

    default refine_grid_layout to false

Src/C_AMRLib/Amr.cpp

commit 31c6cf277c03584049fe048c5bf8e63751e50476
Author: ajnonaka <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 c7021ccc1ff5774800274b747b12a7a1f1d757f7
Author: mzingale <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 2804f225339644017688639d37155d610cbbbc8c
Author: almgren <almgren>
Date:   Thu Aug 20 20:52:56 2009 +0000

    oops -- left in print statement by accident.

Src/LinearSolvers/F_MG/mg.f90

commit 912c90bef9ce3bdfaf264b79124ef83d2b2b97ca
Author: almgren <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 743d2751f136c0b467a66dbc05e54ee11b8fde4a
Author: almgren <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 8e974059cd3e30aff27ded624c8e1c217ef0dff7
Author: almgren <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 3efc3dc156f0c0ec259551ac4f32b03595ed5fc9
Author: almgren <almgren>
Date:   Thu Aug 20 20:47:53 2009 +0000

    Fix fine_edge_resid_1d.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 48cd9cb76e5f12a6d84d20dfc3860657d8b1b0bf
Author: almgren <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 05cc958b4079d066f7d7f46d473c1d81cf3cef5a
Author: almgren <almgren>
Date:   Fri Aug 14 22:28:31 2009 +0000

    Fix indexing in 1d.

Src/LinearSolvers/F_MG/stencil.f90

commit 674716acc8876b505c6ed52c30672d6d5f00e35d
Author: almgren <almgren>
Date:   Fri Aug 14 22:21:48 2009 +0000

    Fix typo.

Src/LinearSolvers/F_MG/stencil.f90

commit 016c6c193c4c5e6d72051061c66d69ae6fd178af
Author: almgren <almgren>
Date:   Fri Aug 14 22:21:05 2009 +0000

    Fix stencil_apply_1d.

Src/LinearSolvers/F_MG/stencil.f90

commit b2aae0d067b188f9cc41f35427b81b46abd6edd3
Author: almgren <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 613cce2f70d86f340f9b0e0de053d914b351c13f
Author: almgren <almgren>
Date:   Fri Aug 14 22:09:47 2009 +0000

    Added 1d capability.

Src/F_BaseLib/fillpatch.f90
Src/F_BaseLib/interp.f90

commit 2006b6408e2cc33284f5839a273feaf92892d911
Author: almgren <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 b7c9dc1e5bbe84d10f12925d63262c6fa9ed594f
Author: almgren <almgren>
Date:   Tue Aug 11 20:28:28 2009 +0000

    Explicitly add climits.

Src/C_AMRLib/TagBox.cpp

commit 592cd0d9642dc96410fad94cb2b5cfc5de1600ae
Author: almgren <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 207f1705fa6df77a7a907eaf7eb4953cda0d7542
Author: ajnonaka <ajnonaka>
Date:   Fri Aug 7 17:16:29 2009 +0000

    added .smp to executable if smp is true

Tools/F_mk/GMakedefs.mak

commit 92f01599045aa7816afbfd8379ea4ea6e86c0427
Author: mzingale <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 55df2de0de028f6868f31720dfb5751a612a9454
Author: almgren <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 bc4941e6dc1ecb03e5802e346d75d807543009be
Author: mzingale <mzingale>
Date:   Tue Aug 4 19:17:19 2009 +0000

    update to reflect new directory locatios

Tools/C_util/regtests/Castro-tests.ini

commit 4da70e99a219082e2b43584df84c60c76c8e46bc
Author: mzingale <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 03c22373481342bb9fab26f3126669a1ead491a9
Author: mzingale <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 b6b12a02139b24ef3f01666a04fead0571a38973
Author: mzingale <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 0dc500228673389562bfa5619592643aef41f19b
Author: mzingale <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 84864e9dccd6be466c397f41a138c70c9a52cce7
Author: mzingale <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 3f2e68813ca700788e2373eedeaf851e0de9cb41
Author: ajnonaka <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 a332d711947ed81c9d9111ee2d930145e72a9b12
Author: ajnonaka <ajnonaka>
Date:   Thu Jul 30 15:40:58 2009 +0000

    mpi stuff for surveyor at argonne

Tools/F_mk/GMakeMPI.mak

commit b4e3a216b2f0264e6b6ce5dd62b0e7c6887cbdf2
Author: almgren <almgren>
Date:   Mon Jul 27 21:50:16 2009 +0000

    Remove unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 1c69cd032c2e7fe4d9f103d0d334dc747f783d4c
Author: almgren <almgren>
Date:   Mon Jul 27 21:48:37 2009 +0000

    Remove extra print statement.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 2f3fc317d05cf87fe5ffe4ebacba94548f7815a2
Author: almgren <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 4480b9d451745ee97b098bdb404bb887037a9fbc
Author: almgren <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 28adade621735e2c0358db2e1397475de0645c46
Author: lijewski <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 3460a6484380d04ec4932b6244a8cb01fe84d759
Author: lijewski <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 22411e8d559aae48284e74f609b1e03b0f8bb61e
Author: lijewski <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 261a950549f988ecdc5e504a6cf167dab1f50273
Author: mzingale <mzingale>
Date:   Thu Jul 23 16:50:07 2009 +0000

    add some useful debugging flags, commented out

Tools/F_mk/GMakedefs.mak

commit 7cc17a5c6ab4202995b710357cd7b1c851d7b776
Author: lijewski <lijewski>
Date:   Tue Jul 21 21:19:21 2009 +0000

    fixed bug in grid_places()

Src/C_AMRLib/Amr.cpp

commit e2b50aa4df96ce1943e37dee0e3769db0cd827ce
Author: lijewski <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 a4975648399e1bca89bd8881216b4f6bfd86136d
Author: lijewski <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 f4a2d46c044d3a02a1ce8c691d81a4e963c1aad9
Author: lijewski <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 b48f5ac079ee403d72d790c6c5bea87d08cb9ef5
Author: lijewski <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 87daa0dfb938de07c0d2aeea49c5913af5284d2e
Author: lijewski <lijewski>
Date:   Mon Jul 13 20:18:28 2009 +0000

    removed simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 301362eeb80f01ff73f210d90b42091613bd906b
Author: lijewski <lijewski>
Date:   Mon Jul 13 20:17:24 2009 +0000

    removed simplify() in GetBndryCells

Src/C_BaseLib/BoxArray.cpp

commit 14702fe97c7b9d1404012c739e915842f02b9704
Author: lijewski <lijewski>
Date:   Sun Jul 12 00:38:32 2009 +0000

    fpb_cache_max_size now defaults to 10.

Src/C_BaseLib/Geometry.cpp

commit 599ff3793b747b13368c3dae299a482e4f20fbdd
Author: lijewski <lijewski>
Date:   Sat Jul 11 03:01:19 2009 +0000

    max_live_tasks now defaults to 50.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 3de6b9cf8706234911005d7e68dfef32780f976e
Author: lijewski <lijewski>
Date:   Sat Jul 11 00:49:21 2009 +0000

    use_copy_cache now defaults to false.

Src/C_BoundaryLib/FabSet.cpp

commit 3d1633722c905b9b348cf959c2dba51b53cec50c
Author: lijewski <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 261756f00f301208f0b4873359062fc4fd2faab7
Author: ajnonaka <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 4064dae38f13e1766cc70de9cd84a75ceef736ec
Author: ajnonaka <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 ea98c321fbecd1d656f2593308fd6ce7eaf0c38b
Author: mzingale <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 e16a9a6781898317cc8a163405770a5aa80f218d
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 19 22:45:25 2009 +0000

    got USE_SMP to compile on intrepid

Tools/C_mk/Make.mpi

commit e9c127903784a1e6f0ff879a96d6836ac4cf1f0b
Author: ajnonaka <ajnonaka>
Date:   Fri Jun 19 22:32:03 2009 +0000

    compiles now with SMP on intrepid

Src/LinearSolvers/F_MG/mg_smoother.f90

commit ffb9be6bdf5b82d4d29d0b0176dfcaaa98e4a532
Author: lijewski <lijewski>
Date:   Fri Jun 19 21:07:13 2009 +0000

    SMP -> USE_SMP=TRUE

Tools/C_mk/Make.mpi

commit 302a157d41fd48cd55a3a8c819e399190f9820c2
Author: lijewski <lijewski>
Date:   Fri Jun 19 19:20:17 2009 +0000

    added simplify() and maxSize() to GetBndryCells()

Src/C_BaseLib/BoxArray.cpp

commit 15a798303d231df3c26a1a709ab4006c26df8c5a
Author: lijewski <lijewski>
Date:   Thu Jun 18 17:16:36 2009 +0000

    more work on intrepid

Tools/C_mk/Make.mpi

commit b8395e8941db769bf19a610fecdc152bb9c51c11
Author: lijewski <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 51ba47ef8ceb8419dd590fe504170e58befa4637
Author: lijewski <lijewski>
Date:   Wed Jun 17 15:54:28 2009 +0000

    *** empty log message ***

Src/C_AMRLib/AuxBoundaryData.cpp

commit 2a08582386b0addfce1a7aa20553efc1abb3772d
Author: almgren <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 7459c78b87befee105718ccb85054d125c75785e
Author: mzingale <mzingale>
Date:   Wed Jun 3 21:02:03 2009 +0000

    update to reflect current problem setups

Tools/C_util/regtests/Maestro-tests.ini

commit 3897e8b118431e95aff938210b31aa4740b6a3d6
Author: ajnonaka <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 0e8d7f58ab3597b8b6752c686cc8bb8732e63eb3
Author: ajnonaka <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 edb7fe14d97e25cc5de69d42aaf67d47edef3f46
Author: lijewski <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 4cc373d1e999b278b25e99e36f8b31ca9a08e511
Author: lijewski <lijewski>
Date:   Fri May 29 23:38:59 2009 +0000

    default verbose to false for CrseInitFinish()

Src/C_AMRLib/FluxRegister.cpp

commit 7f4b3c33fcda1a54602b9f82941a4c6777e7dd48
Author: lijewski <lijewski>
Date:   Fri May 29 23:15:57 2009 +0000

    some instrumentation for CrseInitFinish()

Src/C_AMRLib/FluxRegister.cpp

commit 318e773a3d26d6514f588f5a40b2268382a356d5
Author: ajnonaka <ajnonaka>
Date:   Fri May 29 21:57:03 2009 +0000

    #pathscale friendly

Src/C_BaseLib/FabArray.H

commit c8b8393d67654db0d5ac42135be0892f35eec601
Author: lijewski <lijewski>
Date:   Fri May 29 21:54:15 2009 +0000

    more instrumentation

Src/C_BaseLib/FabArray.H

commit 11c18d8a0af2a0b22e48b37766085db249457c5a
Author: lijewski <lijewski>
Date:   Fri May 29 21:13:35 2009 +0000

    added some instrumentation to CollectData()

Src/C_BaseLib/FabArray.H

commit 1846d1adb4ecb8501974ac9d594dbcd307f5b18e
Author: lijewski <lijewski>
Date:   Wed May 27 21:36:59 2009 +0000

    parallel speedup to linComb()

Src/C_BoundaryLib/FabSet.cpp

commit 9ceeb3995a2d9da3f8f949892812a2eade7d8d7c
Author: lijewski <lijewski>
Date:   Wed May 27 21:08:21 2009 +0000

    parallel speedups for Reflux() and CrseInit()

Src/C_AMRLib/FluxRegister.cpp

commit e2fd24e71af6e2bf0097ba81008e491717185850
Author: lijewski <lijewski>
Date:   Tue May 26 21:02:40 2009 +0000

    added timer to initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 346674bdf9c8e0e1367e237778303856c84d3eb0
Author: lijewski <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 a914af7888eb829cb0ccfa473306db7bb3a68c54
Author: lijewski <lijewski>
Date:   Tue May 26 20:20:52 2009 +0000

    some timers

Src/C_AMRLib/AmrLevel.cpp

commit 6a3dac2372525e537da7a8d5e3289d20b116a920
Author: almgren <almgren>
Date:   Tue May 26 17:19:02 2009 +0000

    Remove unused variables bxa_src and bxa_dst.

Src/F_BaseLib/layout.f90

commit 0552a063cfb4f0a079279cd7bdadb1ef7f2e4a6c
Author: lijewski <lijewski>
Date:   Mon May 18 16:51:25 2009 +0000

    removed unused code in TagBox::coarsen()

Src/C_AMRLib/TagBox.cpp

commit 5e94f55a97bf5ba6ac0f3a278f9d8c8400251067
Author: gpau <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 2e48a2a12f07f73e65473c3d16bb5a03c92a99d7
Author: ajnonaka <ajnonaka>
Date:   Mon May 11 20:57:52 2009 +0000

    added
    
    f90sources += mt19937ar.f90

Tests/LinearSolvers/F_MG/GPackage.mak

commit cd450103545d2c4f8f6b26898220a3a6e2d07d4e
Author: almgren <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 7f69454d13c73b52d14b72d439fd5fe7e08dd435
Author: lijewski <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 c99c6487b5becf30b8ff66cdb8198e6ab290dbdd
Author: almgren <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 c2419fe10c9627b915eca643e3f642fd0dbc8c37
Author: almgren <almgren>
Date:   Wed May 6 23:40:12 2009 +0000

    Fix up stencil...

Src/LinearSolvers/F_MG/stencil.f90

commit f24404069e17b1011e49c7284c479af6992d6cdf
Author: almgren <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 50860bd8a3ff5f48fa423f6e3bece4afb03817a9
Author: almgren <almgren>
Date:   Wed May 6 21:49:33 2009 +0000

    Uncomment lines.

Src/LinearSolvers/F_MG/stencil.f90

commit 384efd5793bd224367cc8c03fbd645a66ca2db99
Author: almgren <almgren>
Date:   Wed May 6 21:37:40 2009 +0000

    Fix stencil in stencil_minion_full_fill.

Src/LinearSolvers/F_MG/stencil.f90

commit 2285fedf469b069c6063f027d38e4aa77c6eb581
Author: almgren <almgren>
Date:   Wed May 6 20:56:00 2009 +0000

    Add stencil for 25-point minion solve.

Src/LinearSolvers/F_MG/stencil.f90

commit 59ead0993997adb87346c005d239d18a75869c63
Author: almgren <almgren>
Date:   Wed May 6 17:27:54 2009 +0000

    Adding stencil_minion_full_fill_2d...

Src/LinearSolvers/F_MG/stencil.f90

commit 4b646da4a693f49c070ff43bf1f72468627a83c5
Author: almgren <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 f51c5d80cd56e4aec8f77d752d6473d02d6928f1
Author: mzingale <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 309bfcd5f312bae29425301bdbd4aef402a7e0d1
Author: gpau <gpau>
Date:   Sat May 2 00:40:33 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileXAve.cpp

commit 967049379251b590d3ce360db54e6d60015fdc84
Author: almgren <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 a5657c1020e907f9db4aa3f85a7ed884fa25ea13
Author: lijewski <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 eb88eccf2620b33ffab5ea8f6120c5269be7fdc0
Author: gpau <gpau>
Date:   Fri Apr 24 19:21:35 2009 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 18e6f200075056ae69db86af5dd87dd430997c47
Author: almgren <almgren>
Date:   Tue Apr 21 19:40:00 2009 +0000

    Fixed verbosity again.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 16ed91fefd875f181aa16e66ecea7c6f5c3921e8
Author: almgren <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 b84fbc08b5df91689e584283bf10942c73839f55
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 21 17:22:08 2009 +0000

    boxassoc deallocate statements weren't being counted properly

Src/F_BaseLib/layout.f90

commit 75bada19d838019b6e4ac4c780c9dbab6193fa25
Author: ajnonaka <ajnonaka>
Date:   Tue Apr 21 17:04:25 2009 +0000

    plugged memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 119b8b0e1a9ef5a23689fafb39f031a5d710ae4b
Author: ajnonaka <ajnonaka>
Date:   Mon Apr 20 22:07:06 2009 +0000

    PathScale with MPI works on jaguar

Tools/C_mk/Make.mpi

commit 248dbbc35c718adc4950a1a475df4dc2f4c05edf
Author: almgren <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 fc24add61f2aa88da6f52de85e944f9db3fdd6e1
Author: almgren <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 7aeeec58dcb44bb3d7e69d037e4fd16b78583e6c
Author: almgren <almgren>
Date:   Mon Apr 20 17:38:34 2009 +0000

    Formatting only.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9d136865b83ad8cff233e471ef8122929f653b43
Author: almgren <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 b1ee9d14d3de5e90f3fb0d47d22acd84132a0169
Author: almgren <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 59a5967a80de77616226339e7fc8dda26d143e70
Author: almgren <almgren>
Date:   Fri Apr 17 21:36:12 2009 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit d65df552fe0f58106948b818ddc49d3b222dec55
Author: almgren <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 b39d3551b9ba1b4e0d06360d68150904ed820186
Author: almgren <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 2cb9fb3e74b5e812261101592947373ea9d29236
Author: ajnonaka <ajnonaka>
Date:   Thu Apr 16 22:20:08 2009 +0000

    plugged memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 1f6c1dc15e57fc4ef2223a3b089366ffada8e2e4
Author: almgren <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 681bd58ecf875ff85a3708ee26442998310b2939
Author: ajnonaka <ajnonaka>
Date:   Thu Apr 16 20:38:46 2009 +0000

    added timer for build_nodal_dot_mask

Src/F_BaseLib/multifab.f90

commit 07bbfec6b6d9d2f00e5f4b77d941b0d3bac23818
Author: almgren <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 12d1932d5e382f51d69d8147b1795f725d2531c0
Author: almgren <almgren>
Date:   Thu Apr 16 17:24:07 2009 +0000

    New stuff for bottom_solver = 4.

Src/LinearSolvers/F_MG/mg.f90

commit 2f76cd05fa0c80b847627540065830ba98efcf05
Author: almgren <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 adf6e8b63bace4b74990699021382695b5820e3b
Author: lijewski <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 474c750e2edb26e2a77533c34a325caabfa98774
Author: lijewski <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 fabba70c8038806246227777ef5cc7027b5243d5
Author: lijewski <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 0757407c75c3d4b163fb7efb046fee0df79fd18f
Author: vince <vince>
Date:   Tue Apr 7 20:39:54 2009 +0000

    added def for HOST if not set.

Tools/C_mk/Make.mpi

commit 1d6edc6f45081adfcc21c4612239384ab6b53521
Author: vince <vince>
Date:   Tue Apr 7 17:37:20 2009 +0000

    updated gojira.

Tools/C_mk/Make.mpi

commit c3c3a9a1a14d806566d73acc5a6c029469fb7b3b
Author: gpau <gpau>
Date:   Sun Apr 5 15:28:42 2009 +0000

    *** empty log message ***

Tools/C_util/Statistics/PltFileXAve.cpp

commit 70e6cbf531af3087cd8130b5d58274bcf36b3d04
Author: ajnonaka <ajnonaka>
Date:   Fri Apr 3 20:38:04 2009 +0000

    better job with timer formatting

Src/F_BaseLib/bl_prof.f90

commit f5d3014d20eaaa7605f7db706070ea8240c896d9
Author: lijewski <lijewski>
Date:   Fri Apr 3 20:19:05 2009 +0000

    *** empty log message ***

Tests/LinearSolvers/F_MG/inputs

commit c35b0d9372d7d197eeceac78fe9bf054b697723d
Author: lijewski <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 666a5f55233dd7d7346d2e5d69d49fbd501f2511
Author: ajnonaka <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 682b4f6e1355caa728b0b06d14bd5cb43daddf83
Author: lijewski <lijewski>
Date:   Thu Apr 2 19:31:52 2009 +0000

    more verbose output

Src/F_BaseLib/layout.f90

commit 9d0d95b6e8ca78be2eeed4f968572e3ae3ed83e9
Author: lijewski <lijewski>
Date:   Thu Apr 2 17:20:29 2009 +0000

    added simple hash to speed up copyassoc matches

Src/F_BaseLib/layout.f90

commit 22c09fc4739227fdf2845d20b4132d99aff37cf0
Author: lijewski <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 8a586e5e342b802d85536e959dfd05cb021c5c41
Author: lijewski <lijewski>
Date:   Wed Apr 1 20:54:14 2009 +0000

    more sophisticated cache clearing strategy

Src/F_BaseLib/layout.f90

commit 327be62db3f5c5c841896585d9335f4343480a11
Author: lijewski <lijewski>
Date:   Wed Apr 1 20:24:24 2009 +0000

    smarter about what to delete from copy cache

Src/F_BaseLib/layout.f90

commit 1eeaa91ab8ac85940e471907be19f7faada993fe
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:23:20 2009 +0000

    print copy cache stats on flush

Src/F_BaseLib/layout.f90

commit 034aa3b0514a3007fdde95813e74aeb85165d5e9
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:12:35 2009 +0000

    copyassoc cache refinements

Src/F_BaseLib/layout.f90

commit c9cc1b4a6f715c3ad7e96d53266041c19cce1537
Author: almgren <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 9df2b60113c9f3b45ace1cb8177e97c4618e8c68
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 31 17:24:05 2009 +0000

    fix comment

Src/F_BaseLib/make_new_grids.f90

commit 9e71ff410498c1773dac529c0668d5dbfba49ba1
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 31 17:09:01 2009 +0000

    fixed a comment

Src/F_BaseLib/ml_boxarray.f90

commit 377327506c52b27046ed12e746a258981dc4d9dd
Author: lijewski <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 4edc638758e12f5b4ba59c8cd0f832b79262c21f
Author: lijewski <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 471403705caa75958824a5ebf9ccea332b0903c9
Author: ajnonaka <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 fdecf5123521090841aea784035f1c665946988b
Author: almgren <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 603752e1557ef8fac438a1c38325e73847967e2b
Author: ajnonaka <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 58419fb5d4b77c8646adcf04c4f1ce2aa7494af4
Author: almgren <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 fdd442328422596b2d0cc75087d593b51b314695
Author: lijewski <lijewski>
Date:   Mon Mar 30 17:51:45 2009 +0000

    set sfc_threshold default to 0

Src/F_BaseLib/layout.f90

commit 536640ff3228144f208bc23dabffeab76533c02a
Author: lijewski <lijewski>
Date:   Mon Mar 30 17:47:33 2009 +0000

    turn off do_mcc by default

Src/F_BaseLib/knapsack.f90

commit 417cc25b5e91267550d7a72fe730894b9dd282d5
Author: lijewski <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 cff9a168a492703d361e6f5577145394a4456c18
Author: lijewski <lijewski>
Date:   Sat Mar 28 22:19:10 2009 +0000

    commented out some print statements

Tests/LinearSolvers/F_MG/cc_multi.f90

commit 5d1e079132132ce525d22685f28767d874ce3084
Author: ajnonaka <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 1048c1636528f629459a69a8497af2e4febafeb6
Author: lijewski <lijewski>
Date:   Fri Mar 27 20:06:42 2009 +0000

    remove bl_prof_timers

Src/LinearSolvers/F_MG/mg_smoother.f90

commit ef541865fd6068b6394ec1b91dc8ecad1dc516dd
Author: lijewski <lijewski>
Date:   Thu Mar 26 21:58:34 2009 +0000

    modest speedup to SSFC stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 7594644bc2ef73630546711da7aa67f972e7cc85
Author: lijewski <lijewski>
Date:   Thu Mar 26 17:51:53 2009 +0000

    modest optimization to sfc_greater_i()

Src/F_BaseLib/knapsack.f90

commit 92a1a58a614fbbb880438a106427b825fa01a355
Author: lijewski <lijewski>
Date:   Wed Mar 25 19:57:25 2009 +0000

    minor tweeks to previous fix

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit b3d62f850ff00df5cf24879f484fe48a0d74240c
Author: lijewski <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 393409c8332ef94d21ec682343a43b117ab18ae4
Author: ajnonaka <ajnonaka>
Date:   Tue Mar 24 21:45:48 2009 +0000

    make modules go to correct directory on jaguar

Tools/F_mk/GMakedefs.mak

commit 186957fc1cc1e93be42f2ebea7f9f25e5618afab
Author: lijewski <lijewski>
Date:   Tue Mar 24 20:23:35 2009 +0000

    efficiency mods to layout_get_box_intersector

Src/F_BaseLib/layout.f90

commit d25f832c09532fffb5f30559e06269775bf99927
Author: lijewski <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 b6efad6c58072b1d9633b150af4c5dd8c1e9feda
Author: ajnonaka <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 9be351ae4b21d686509fe40701ec7be362069284
Author: ajnonaka <ajnonaka>
Date:   Sat Mar 21 00:07:10 2009 +0000

    made knapsack verbosity false by default

Src/F_BaseLib/knapsack.f90

commit d5061d679355910dcc8a93e275a2ebe02b642a3f
Author: lijewski <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 dbe393cf17eb978cb9f51d7ccc5d59d1c2d5059c
Author: almgren <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 94ebf575c10d5dc0c455becd9771faa8e463b26b
Author: vince <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 0fbdcebfc5bf5f43ec2c1f1460ea7ae914adb573
Author: almgren <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 56225ac7e0dcfd644d48f51e519602eab9d61a10
Author: vince <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 f91de45446707f6f32403e92677ec7c02269b7e1
Author: lijewski <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 db86c16fa8c682ee1373513fa2a1f738a7028510
Author: almgren <almgren>
Date:   Tue Mar 10 20:09:21 2009 +0000

    Make the derive functions virtual.

Src/C_AMRLib/AmrLevel.H

commit f0c59916a95b818b76f9992c550206e29ddfc895
Author: lijewski <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 d437ce703ab207671763d0bf593a28954544bfcb
Author: lijewski <lijewski>
Date:   Tue Mar 3 20:34:29 2009 +0000

    some cleanup

Src/C_BaseLib/DistributionMapping.cpp

commit d7615cba6246feb9d3f1ebe609be64e84aa0f6de
Author: lijewski <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 967b59f691fc1cfd487ee949511901a641d98707
Author: lijewski <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 c176a6cf8ab5566678527b7b442c28ed73d3b380
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:18:37 2009 +0000

    put FSRec in unnamed namespace

Src/C_BoundaryLib/FabSet.cpp

commit a4db4d1abba5c43777e9a24b1aa6aebe310173e3
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:17:55 2009 +0000

    use IntVect::Compare instead of IntVectComp

Src/C_AMRLib/TagBox.cpp

commit a796c49b8897bd75d1c62daddd4f287680ceef0c
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:17:29 2009 +0000

    put struct in unnamed namespace

Src/C_AMRLib/FluxRegister.cpp

commit b652594b5a92d0845f7311e88b42357ac8d1eb64
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:04:12 2009 +0000

    put BoxCmp in unnamed namespace

Src/C_BaseLib/BoxList.cpp

commit 551b2e2e779039f9b4f762218483169072de201a
Author: lijewski <lijewski>
Date:   Mon Mar 2 21:00:59 2009 +0000

    put SFCToken in unnamed namespace

Src/C_BaseLib/DistributionMapping.cpp

commit 2dfac20eb407fc1f40623e0965ca9ee5a0c6cb6a
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 27 23:31:54 2009 +0000

    mpi works in 3d now on lawrencium

Tools/C_mk/Make.mpi

commit 0b2f8ff4a798ab02c1eadfa31009d942085e38b9
Author: ajnonaka <ajnonaka>
Date:   Fri Feb 27 23:21:11 2009 +0000

    catch mpi for lawrencium

Tools/C_mk/Make.mpi

commit b242781a43707f6324a122f4c8ca6c94bdd16052
Author: marc <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 6ed34cc6b7610636613b772eeb4243646e3f74f6
Author: ajnonaka <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 ac55e2122fe9b76da72d2670b14c14872484304f
Author: mzingale <mzingale>
Date:   Mon Feb 23 18:51:57 2009 +0000

    if making benchmarks + compileTest, nothing to report

Tools/C_util/regtests/test.py

commit 1f2066822b3c1aa56e2c91daf1c15db8f0961235
Author: mzingale <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 b20c1f5f422577071a6b8aaaaa5d47283a871bbc
Author: lijewski <lijewski>
Date:   Fri Feb 20 18:20:15 2009 +0000

    update for pleiades

Tools/C_mk/Make.Linux

commit 187b2bcac1af192286f81051521b9943b3c0417a
Author: almgren <almgren>
Date:   Thu Feb 19 18:34:45 2009 +0000

    Fixed settings for pleiades.

Tools/C_mk/Make.mpi

commit f4724add99430c816bbdac6addaf29543c244c00
Author: lijewski <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 26b256405fc3968d12b6b8215a61e015891e1cba
Author: lijewski <lijewski>
Date:   Tue Feb 17 23:50:36 2009 +0000

    some work on implementing space-filling-curves

Src/F_BaseLib/knapsack.f90

commit 68ed7b64cb56eb4b6a0293b6742d92795dbbeec8
Author: lijewski <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 c26fe79e39aa42514b2d0f6c7bf193c3e26afaf3
Author: lijewski <lijewski>
Date:   Fri Feb 13 16:39:52 2009 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 65fec44ed0374be368ca2dba2b2ea7352595b9be
Author: almgren <almgren>
Date:   Thu Feb 12 21:13:02 2009 +0000

    Add BL_USECLOSE for pleiades.

Tools/C_mk/Make.mpi

commit c4e291f0fcad55a502d72a6b3f4a8d5687313fe2
Author: almgren <almgren>
Date:   Thu Feb 12 21:11:32 2009 +0000

    Add special case for pleiades.

Tools/C_mk/Make.Linux

commit c7af4cb7ba75ada87fab2076e16074803953f1e0
Author: vince <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 f5d3a017772a869f9b0e80f2134ee571d6ae2f5d
Author: mzingale <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 fe3f89be2650fa8e797ee51a287e6888e9ebe553
Author: marc <marc>
Date:   Wed Feb 11 23:06:50 2009 +0000

    fix data type

Src/C_BaseLib/ParallelDescriptor.cpp

commit 201593cb05d37f6f7413e613a3bf42e4c01c1fe4
Author: mzingale <mzingale>
Date:   Wed Feb 11 22:02:16 2009 +0000

    add support for compile-only tests

Tools/C_util/regtests/test.py

commit c6e479dc6997367a4583ead73320e022c36c757e
Author: lijewski <lijewski>
Date:   Wed Feb 11 01:44:06 2009 +0000

    replaced STOP with bl_abort()

Src/C_BaseLib/BLutil_F.f

commit 67145c6c1aabf7046eceb139b95e490fd1731de3
Author: lijewski <lijewski>
Date:   Tue Feb 10 21:49:11 2009 +0000

    added some xlC/xlf stuff for intrepid

Tools/C_mk/Make.Linux

commit 6825d9fe2d96d9b813ee61bb5c2c4ded55b63b32
Author: mzingale <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 a6bf07fe00f4e1f2c02ceb75f1033dad8530317a
Author: gpau <gpau>
Date:   Mon Feb 9 21:09:08 2009 +0000

    Fixes for Lawrencium.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 8df5a8cc677b6f824dd4c209ffad3b58a36c2d1a
Author: ajnonaka <ajnonaka>
Date:   Mon Feb 9 20:30:54 2009 +0000

    works for Lawrencium mpi

Tools/F_mk/GMakeMPI.mak

commit 123204860dec4c424cc18ce74891e581bb1378dc
Author: mzingale <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 ad193dae2966734c655bed3fe4f878666934b8e5
Author: mzingale <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 5e348a53ae88a10164676b191ea8883c1c96ff76
Author: vince <vince>
Date:   Fri Feb 6 22:57:03 2009 +0000

    changes for lijewski.

Tools/C_mk/Make.mpi

commit 7107e49148d62fc90c26ae0d5120ed8e544e334f
Author: lijewski <lijewski>
Date:   Fri Feb 6 22:14:38 2009 +0000

    Do_AllToAllV is now settable

Src/F_BaseLib/multifab.f90

commit 093bf5ba34bbd9da5641689815ea63615839e3c7
Author: lijewski <lijewski>
Date:   Fri Feb 6 21:30:57 2009 +0000

    some rearrangement

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 13b9e51a50840a47dfe94871dd25567c5f413dcf
Author: mzingale <mzingale>
Date:   Fri Feb 6 20:58:08 2009 +0000

    Chris's Intrepid changes to get Amrvis compiling

Tools/C_mk/Make.defs

commit 746e1827e267d53dc4cebe412f636188e5f91458
Author: almgren <almgren>
Date:   Fri Feb 6 20:46:19 2009 +0000

    Fix previous fix.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 6cd0bbac9c8f1d4f342fc8d0c0930d25961b6ba8
Author: lijewski <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 0001436b2a14356c00aea3d10802513bf2252285
Author: mzingale <mzingale>
Date:   Fri Feb 6 16:30:50 2009 +0000

    more clean-ups

Tools/C_util/regtests/test.py

commit 78aab489f1a223c77a60746f76e8bedb764c4e7b
Author: mzingale <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 079ecbb4ecf1d0d1c73fc46b09d553baf12cee03
Author: mzingale <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 d835c161557b0111512a61ec9a4cc075f507e682
Author: mzingale <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 26eb725829abff46e324720b89de5ca90c973fb4
Author: mzingale <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 065daa5cf3339f40a3d617943e9c939c83e3110e
Author: lijewski <lijewski>
Date:   Tue Feb 3 17:08:10 2009 +0000

    note in comments that if you want Array<bool> use std::vector<bool>

Src/C_BaseLib/Array.H

commit 5f63a477a7f593a97837c50a7149cb6f4c9cccdd
Author: vince <vince>
Date:   Mon Feb 2 20:50:44 2009 +0000

    intel 11.

Tools/C_mk/Make.defs

commit 0c9a08845607a01c3d718d69dcfa8bc07186194a
Author: mzingale <mzingale>
Date:   Sat Jan 31 20:04:00 2009 +0000

    add a comment

Tools/F_scripts/make_build_info

commit a9d95e2b89af9a1054f0ff2438313c0f5d25b734
Author: mzingale <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 80a07b4cf4b745e4650b266b7037decd536b2fdd
Author: lijewski <lijewski>
Date:   Thu Jan 29 21:13:24 2009 +0000

    added BL_NOFAST to turn off maximum optimization

Tools/C_mk/Make.Linux

commit b5d6d1f0d4be6d4dc2a0693c4126686614f2e500
Author: lijewski <lijewski>
Date:   Thu Jan 29 17:47:15 2009 +0000

    removed STRCTLY stuff

Tools/C_mk/Make.defs

commit 96887610be23373bceeba6433c1cf01c2775f184
Author: mzingale <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 9b722c15832e68b985b48f7f412facbbf393db70
Author: mzingale <mzingale>
Date:   Wed Jan 28 18:00:20 2009 +0000

    make the vis stuff more robust

Tools/C_util/regtests/test.py

commit 22f5a4e3d064140aa98e184df1263df5b92620ed
Author: almgren <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 0d872cf5f53029cb8471af0408a010614f77d838
Author: almgren <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 4fa190687ef65628d5e61e2f431d171a68c7070f
Author: almgren <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 7a6fc9978d89352a1ee3b7dd7970a72401b42e55
Author: mzingale <mzingale>
Date:   Thu Jan 22 21:21:02 2009 +0000

    f90 -> f95 on intrepid

Tools/F_mk/GMakeMPI.mak

commit 16826b2716aeb647fe230d44e6d469b5c5fcdb77
Author: mzingale <mzingale>
Date:   Fri Jan 16 20:28:01 2009 +0000

    add Chris's ANL Intrepid fixes

Tools/F_mk/GMakeMPI.mak

commit d4c04a99ff4bffe53271791349db33198b1be0f5
Author: lijewski <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 ca0309e8838dee047bfd842b5d4b20fba7816d76
Author: almgren <almgren>
Date:   Mon Jan 12 22:19:31 2009 +0000

    Removed unused variable.

Src/LinearSolvers/F_MG/ml_cc.f90

commit d24b33412d353ae0d29c7f019766f02829fca685
Author: gpau <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 2601ae6bd9a8426ce714fc4ec8736bf957676733
Author: ajnonaka <ajnonaka>
Date:   Fri Jan 9 23:41:34 2009 +0000

    forgot to declare a variable

Src/F_BaseLib/fabio_c.c

commit f08957ae03ecfd050e1d1c260e1e64807aa940c0
Author: vince <vince>
Date:   Mon Jan 5 21:12:15 2009 +0000

    added varan.

Tools/C_mk/Make.mpi

commit b4f846ae4b8e9061cb7b3dfb14c71efabbed9791
Author: mzingale <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 6ed8278a5837779116731c4002b56e75fdf767ff
Author: lijewski <lijewski>
Date:   Fri Jan 2 18:13:04 2009 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/mg_cpp.f90

commit de3c957c32278521317a2d1e31d8ad1152aa0207
Author: almgren <almgren>
Date:   Sat Dec 27 01:47:51 2008 +0000

    Clean up some memory.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 64298f3f524fa414f46647f0175a9bba14e09067
Author: lijewski <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 82c47066bc0dfc637a30d32f70d45afe0a66b83f
Author: vince <vince>
Date:   Wed Dec 17 21:52:22 2008 +0000

    added F90 for franklin.

Tools/C_mk/Make.Linux

commit 71972fc320ace9dd31dca1c64e7ba80408fa06ad
Author: lijewski <lijewski>
Date:   Wed Dec 17 21:00:35 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit a2f76dcdd10e9fac3309a68a7e58870e3e299cf2
Author: almgren <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 d6744cb896abf9c675685fc651fd82047f552415
Author: ajnonaka <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 753e47c79da33eba57ec9490fab9a1e1855db9ee
Author: almgren <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 b55945aa26da79b1633c00a4381f7934c50098cc
Author: almgren <almgren>
Date:   Thu Dec 4 18:40:43 2008 +0000

    Pass abs_tol through into solver.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 6a7f1823c2e15f5d5e6953ed9bea82029a3328a8
Author: almgren <almgren>
Date:   Tue Dec 2 01:51:59 2008 +0000

    Cleaned up SETAREA.

Src/C_BaseLib/COORDSYS_1D.F

commit c8ecbcabcc529c74e90619ac06b049d0dfa55358
Author: almgren <almgren>
Date:   Tue Dec 2 01:51:28 2008 +0000

    Cleaned up SETAREA

Src/C_BaseLib/COORDSYS_2D.F

commit 191633c6d3bb4441ff2f9dc359bcdf9ed74ece24
Author: almgren <almgren>
Date:   Tue Dec 2 01:49:30 2008 +0000

    Cleaned up SETDLOGA.

Src/C_BaseLib/COORDSYS_2D.F

commit 1478959eb1ec056d7a10f1a96937e264ee8b7284
Author: almgren <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 4681df6eb8c1910bd65703189f89e070e39954f1
Author: lijewski <lijewski>
Date:   Mon Nov 17 23:45:55 2008 +0000

    ParmParse do_full_knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit 16d92f480062c4071e3e5c44678bcd8fa9868779
Author: lijewski <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 bc4d107d8799ba47a25d34f062db133c2b4c7328
Author: lijewski <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 c6c9e38196aade7a4f6f02709ebae3ef7beffe14
Author: lijewski <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 f19ca1d83d07c1b7343464b50e7803f85587c8be
Author: lijewski <lijewski>
Date:   Wed Nov 12 04:27:32 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp
Src/C_BaseLib/Geometry.cpp

commit 435ac2b24ce2c1af897715e23d8c34b489875447
Author: almgren <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 bb5bf0a570a2f739d26a3e1148fa53b3895339a9
Author: almgren <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 b2fd11f6b1b45845cc620a4631bd33fdde4ab6ab
Author: almgren <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 c65db7f1fb0210875101f9898140a0a6670d3369
Author: almgren <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 b3391798c74762a79ec6e9650a668e8587bf5d78
Author: lijewski <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 efb6dc75b797f5d594e07109567b494870ba26ba
Author: almgren <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 bbc057ae27ac5186789d8e3fefe5cfa0f4d6b530
Author: almgren <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 16a4cabe1eda0664983a425c598f167786851094
Author: lijewski <lijewski>
Date:   Wed Nov 5 00:10:43 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 323b27654e7699b2acb1862d2606dacd524079fe
Author: lijewski <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 f6c35a25196b4290ef4bc4358a81299bff4ee05a
Author: lijewski <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 c23bcecf408d89b73c0b6098797c909d03a85147
Author: lijewski <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 93dafa147ae8dcbb8f8341feb9ca5f5754175db6
Author: lijewski <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 ae50b387bb185ecb1ec7a254db7d373c3bcc3f30
Author: sepp <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 96dc30c89092a8e1e100b2f09ae048f1a432c7de
Author: sepp <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 d49756f1c210065569cd195782c75394d8882df7
Author: lijewski <lijewski>
Date:   Fri Oct 24 21:05:35 2008 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 74e65e566c81b7750392918b9c4aa16f805262b5
Author: lijewski <lijewski>
Date:   Fri Oct 24 03:47:29 2008 +0000

    skip over orphaned DMs in GetMap()

Src/C_BaseLib/DistributionMapping.cpp

commit cacb13368166af858f6e8bf20fd68b99f72cb5d3
Author: vince <vince>
Date:   Thu Oct 23 19:56:37 2008 +0000

    added gigan.

Tools/C_mk/Make.mpi

commit 679e912bfc76e05b4ca3edb14cbe90446a9a01c0
Author: ajnonaka <ajnonaka>
Date:   Wed Oct 22 22:45:44 2008 +0000

    fixed bug in index-ing

Src/LinearSolvers/F_MG/nodal_divu.f90

commit d21050664aec7f07a8f7a8e6db7fe45da1ccfead
Author: lijewski <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 b292b0bfa71fb3fa30dd37a4facf2a03c6ce1f2d
Author: almgren <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 f8aa543ebbf719e74b0fb1ea5dd73376ac866ce2
Author: almgren <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 3154f8627ab03d50668f9db941d07c5650433441
Author: almgren <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 feb59541df799abbc6c5ae1709a7331c050f0ab5
Author: lijewski <lijewski>
Date:   Thu Oct 16 18:13:23 2008 +0000

    reverted back out recent GetBndryCells() changes

Src/C_BaseLib/BoxArray.cpp

commit 9b8b5dd7b03407c366e307c0937f9b58a3bec6ac
Author: lijewski <lijewski>
Date:   Thu Oct 16 16:03:01 2008 +0000

    Do a maxSize(64) after simplify() in GetBndryCells().

Src/C_BaseLib/BoxArray.cpp

commit 346ff2b71a7f5b2bf3cd0b1f016e3fdb7d4bbf99
Author: lijewski <lijewski>
Date:   Thu Oct 16 16:02:32 2008 +0000

    Do a maxSize(64) after simplify() in initialize().

Src/C_AMRLib/AuxBoundaryData.cpp

commit d55a8de59e1208c7b270daccb28e019e7c606c7f
Author: lijewski <lijewski>
Date:   Wed Oct 15 22:45:30 2008 +0000

    GetBndryCells() now does a simplify().

Src/C_BaseLib/BoxArray.cpp

commit 2d79a45edbc47d3e6aedf4ed341cf2b73f6d05fb
Author: lijewski <lijewski>
Date:   Wed Oct 15 22:43:34 2008 +0000

    now do a simplify() in initialize()

Src/C_AMRLib/AuxBoundaryData.cpp

commit 892a1bda727bdcdd38974ff76e269bcaac7f9ba3
Author: marc <marc>
Date:   Sat Oct 11 00:23:53 2008 +0000

    Add default flag to Mikes FPB code interface

Src/C_BaseLib/Geometry.H

commit c951c4e9282ce5ae0618f4767e9797f42e94ec96
Author: lijewski <lijewski>
Date:   Fri Oct 10 23:31:57 2008 +0000

    now use Ofast for PathScale optimization

Tools/C_mk/Make.Linux

commit bb5f1d11d40764465429f215571cd8a616ace70a
Author: lijewski <lijewski>
Date:   Fri Oct 10 22:35:41 2008 +0000

    FillPeriodicBoundary() is now a template in BoxLib namespace on FabArray<FAB>
    ----------------------------------------------------------------------
    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 25ca197400ff679d1a365238017d8fea3639a3d1
Author: lijewski <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 8fa248285f8f4b29008685fb4cdfd311e134222c
Author: ajnonaka <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 a573d1eb2896ee8ab6acdfeb8b5c96217a8ad908
Author: ajnonaka <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 0e3b4503be4f911e751f220c018389fbca73c953
Author: ajnonaka <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 4ea4a97ed0768e62a6da82b07eaeb9cd162f31da
Author: ajnonaka <ajnonaka>
Date:   Sat Oct 4 23:12:47 2008 +0000

    oops; franklin's hostnane is nid*.  works now

Tools/F_mk/GMakedefs.mak

commit c41cbdaeb6535d6ef660bed9ecfca3a6b77ae64d
Author: ajnonaka <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 c5aa39ae49e3c6ddba36740b06126fc4defb7acb
Author: almgren <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 baf0d347a536aba67f09f2fe7a7198e03e0762ec
Author: almgren <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 26145cd254806f9d92a118f85c04b7b5d9db1c6e
Author: lijewski <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 4b448b76e601e3fe7f39f2524121b9e901054326
Author: lijewski <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 3be26e3dec7ea32ebb9a525b350fda6ef4ab4265
Author: mzingale <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 d00932bed7b8b930cd0ff8f2c5014e8152f52165
Author: almgren <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 45c555c585ac3fae52bf09b447aa289a516272ea
Author: vince <vince>
Date:   Thu Sep 25 22:50:21 2008 +0000

    strstream update.

Src/C_AMRLib/DatasetClient.cpp

commit fc9995ace0dca662a08376f1331667c1a1358f27
Author: sepp <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 aa310321f9cc5166d2d12c27686161757e70a0f9
Author: ajnonaka <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 5fc0995501fc05611a2e4dda02b1183fc44eb105
Author: ajnonaka <ajnonaka>
Date:   Mon Sep 22 18:35:33 2008 +0000

    f90sources += mt19937ar.f90

Src/F_BaseLib/GPackage.mak

commit e9c9e70773fe04a735da91fc91ff1f33fbbacfeb
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 17 20:49:05 2008 +0000

    added mpi capabilities for atragon

Tools/F_mk/GMakeMPI.mak

commit 5d68e5215856ab722f56ae402f659140091e3cf3
Author: vince <vince>
Date:   Wed Sep 17 20:01:52 2008 +0000

    added atragon and gojira.

Tools/C_mk/Make.mpi

commit 67978532c439d3c95381e5d204031f0ceaef165d
Author: ajnonaka <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 e4897a6163114380b828a3a86c6ab5995bf6be16
Author: ajnonaka <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 8bcfd2c3b8ffcc01cb41cc62b0466e6c9ad4ebab
Author: ajnonaka <ajnonaka>
Date:   Wed Sep 10 21:11:17 2008 +0000

    made the cpy_ functions public

Src/F_BaseLib/multifab.f90

commit a90c425976f93210c6814b5a22047173905826e5
Author: ajnonaka <ajnonaka>
Date:   Mon Sep 8 19:39:20 2008 +0000

    works for ng = 0

Src/F_BaseLib/fillpatch.f90

commit 035dbab7063e7e23489ec5964ff2c85480fea5df
Author: lijewski <lijewski>
Date:   Mon Sep 8 19:26:20 2008 +0000

    fix for case when ng==0

Src/F_BaseLib/fillpatch.f90

commit b091b92eea5bccfc9724c2913953b91f5c8fd631
Author: marc <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 e97ff3133deb11f732dc9beedc82615c9e444606
Author: marc <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 f671e701716bd03cb0013fe8b1d6062b72b7fe0d
Author: ajnonaka <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 8f9532eb4e889257a048787ca7a1d05f36a65598
Author: ajnonaka <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 52a03e2ac832608a78bfcdd78e6baff64850b4ba
Author: almgren <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 2fb4421f21fb70072fc0f7ceb5ae47b1fd020fa1
Author: ajnonaka <ajnonaka>
Date:   Thu Aug 28 17:41:48 2008 +0000

    made 2d consistent with 3d

Src/F_BaseLib/tag_boxes.f90

commit 23bd38798627082c9514cbff581862c8ca6690a7
Author: ajnonaka <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 ce7f03654efcfce24f62e6c9a39398f942d59ec0
Author: ajnonaka <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 84316eb951ed7fc7dd10ebabd9eacfbd9c1967f3
Author: mzingale <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 a66c30c22d9d7e39f6a76594f77709df8d5a5b5f
Author: almgren <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 0b45ae200ecbbd67ffd5f6d933ac7d2815794e6d
Author: almgren <almgren>
Date:   Mon Aug 25 23:07:31 2008 +0000

    Replace "area" by "coeffs"

Src/LinearSolvers/C_to_F_MG/MGT_Solver.H

commit f80d6385d4c0d71471a979f112a1dfebae6926ae
Author: almgren <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 4061b1840c7af057d4447c0fdc2fb1639ee849f7
Author: mzingale <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 646f8b4fab30a69ba1e669f26c089154c8800080
Author: almgren <almgren>
Date:   Mon Aug 25 20:12:10 2008 +0000

    Add mgt_applyop.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit bd4b6bb264a5af206ebedb71a76cbcf680b0e8a6
Author: almgren <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 f5e8dacccdec403795ffeb746c6ed92f47ff31ea
Author: almgren <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 c61d21d702eb0877b809e25b4fb965babd596aeb
Author: almgren <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 bc32640ec56419ebc5717b23a14920d875a88868
Author: ajnonaka <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 9a32789a8af6161080c0d6d1e0c79603414a3a31
Author: mzingale <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 af1a1e43012e163a7cea716f5c4606a24d8614b7
Author: mzingale <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 ba34f6f192d85759444c8d3e5f5afad157760583
Author: mzingale <mzingale>
Date:   Mon Aug 18 03:10:01 2008 +0000

    start adding the framework for visualization

Tools/C_util/regtests/test.py

commit 16b229e9bc4f567b62534c89a221cb972d891122
Author: mzingale <mzingale>
Date:   Sun Aug 17 23:19:46 2008 +0000

    update to reflect dx = dr changes

Tools/C_util/regtests/Maestro-tests.ini

commit e3ecde60743c4ccc590ef422794d7f19a66a194a
Author: vince <vince>
Date:   Tue Aug 12 00:09:49 2008 +0000

    added battra.

Tools/C_mk/Make.mpi

commit fafe59ebf67ddba4c93477b8fa86759ab67547ca
Author: vince <vince>
Date:   Mon Aug 11 19:18:06 2008 +0000

    changes for manda.

Tools/C_mk/Make.mpi

commit 8d2a74a0e1cf675c16c5fe7a65cb8c0b386fce17
Author: almgren <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 48b21e006a6732ddf233718ed03f5e05e6b65921
Author: almgren <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 cf07c6d2dc671087be5a82cf77900291e584f0bc
Author: almgren <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 7755c58a31472bcfa1f703c3e49b43c5151ccc81
Author: almgren <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 d91ad504193d67ef7baae780f4ca4fc72569dbfc
Author: almgren <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 485a63857ae0e44a584bbb2a1cbc0f050f04bdc8
Author: vince <vince>
Date:   Wed Aug 6 19:38:44 2008 +0000

    changes for naphta.

Tools/C_mk/Make.mpi

commit 1adb427518e94f75ee99fc0f1f60c3bf1e4b5cf4
Author: almgren <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 7d2531b735fc08e4c2364e7b92873c2ed76c5e58
Author: almgren <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 e4b4232cd1f23401501249eec7ce16d65f4c42eb
Author: vince <vince>
Date:   Wed Aug 6 18:30:25 2008 +0000

    change for naphta.

Tools/C_mk/Make.mpi

commit 708db2a10156407659a68fd4707aef58f4c688a6
Author: lijewski <lijewski>
Date:   Wed Aug 6 16:16:23 2008 +0000

    destroy() tagboxes in enforce_proper_nesting()

Src/F_BaseLib/make_new_grids.f90

commit a8418e407cce6a50095fb3badfcdd9155f742480
Author: almgren <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 aa8ca7f75373d482b9d43e805ec93e77ea224bf2
Author: almgren <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 68e4e88d203c538e81c69c463eaa2372b75d8bba
Author: almgren <almgren>
Date:   Wed Aug 6 00:03:36 2008 +0000

    Moved enforce_proper_nesting into here.

Src/F_BaseLib/make_new_grids.f90

commit 225134ef0651f0d76ce54bc7bf09a71437fa94cd
Author: almgren <almgren>
Date:   Tue Aug 5 23:01:46 2008 +0000

    Set minwidth = 4 instead of 2.

Src/F_BaseLib/make_new_grids.f90

commit 83153f9de14832df7d604d57d3b6cff9fab5d7c0
Author: almgren <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 5389d911545b12561bcfa2070d1a67e30f1502bc
Author: gilet <gilet>
Date:   Tue Aug 5 18:08:43 2008 +0000

    mpich now works on gigan

Tools/F_mk/GMakeMPI.mak

commit a7934c8e6cc9ceda0f97b0fa9f5e01fee738086a
Author: almgren <almgren>
Date:   Mon Aug 4 23:19:06 2008 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 640ac8416263be1510ba7a3e63cfa64e68e19067
Author: almgren <almgren>
Date:   Mon Aug 4 23:13:02 2008 +0000

    Fix a typo.

Src/LinearSolvers/F_MG/stencil.f90

commit f3d5f0250ca80c94c823236ff048ac8c698be699
Author: almgren <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 2b6258d09dc0bcf0b8f8e8e07e53e00bde7a4928
Author: almgren <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 790357b38c9182f0c6ac549db579345957a0cfc1
Author: almgren <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 3c09bf2e7a9541165ca6d50dcfae76c3e5c2c973
Author: almgren <almgren>
Date:   Fri Aug 1 23:11:45 2008 +0000

    Remove unused "proc"

Src/F_BaseLib/cluster.f90

commit bdfb9e9ff13bfedad200e2ee412e1095963fdf6e
Author: almgren <almgren>
Date:   Fri Aug 1 23:11:02 2008 +0000

    Remove unused ibxs(:)

Src/F_BaseLib/cluster.f90

commit 6b62b6f60f27978bc7a10fe9dd0fa05e4d3c517f
Author: mzingale <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 f35bf0d517568ada0905378d9067499ea1e7472e
Author: lijewski <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 0f9a1945b8d73fe37b17a11f08c21647bb961955
Author: almgren <almgren>
Date:   Thu Jul 31 20:42:51 2008 +0000

    Replace bl_abort by bl_error.

Src/LinearSolvers/F_MG/mg.f90

commit 058510e6f15e9eca9d2d70ab591a42ec580fc4ef
Author: almgren <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 656387ad9ac29a88cdae9233e631f85cc9cadcba
Author: lijewski <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 cf294860482090be729e1f7cd071d3669c6a63b1
Author: almgren <almgren>
Date:   Thu Jul 31 17:54:27 2008 +0000

    Put new mpi link for manda only.

Tools/C_mk/Make.mpi

commit e93c03477c91e178e45cd65eb3eabb1981fc41a3
Author: almgren <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 cb7f22c3b331ed067a521f29cdc92fb47b3df93b
Author: almgren <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 2c5d2c8b998a46f35a854b2626931b0e4ab2f786
Author: lijewski <lijewski>
Date:   Wed Jul 30 01:10:47 2008 +0000

    littlea cleanup

Src/C_BaseLib/BaseFab.H

commit a6e64fa65437b8c283b68fd65a0a444c9e26f405
Author: lijewski <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 c71ddb25e26de9099ca2fed8184da7f586b2a47c
Author: almgren <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 b1ce4d38555d751232e27b5ee2e8c3b4f8caadc2
Author: lijewski <lijewski>
Date:   Tue Jul 29 16:28:08 2008 +0000

    modest simplification

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit 77ea1474e6ad45aeb02af2976fe54b21241e2b6f
Author: lijewski <lijewski>
Date:   Wed Jul 23 21:38:57 2008 +0000

    some memory cleanup

Src/C_AMRLib/AmrLevel.cpp

commit 4c2b27f5743cb65bf69cd8a6be8611f9507ac826
Author: lijewski <lijewski>
Date:   Wed Jul 23 17:18:34 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit ed2dd69a7ef144605aa7ac15342f870dee855d8e
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:45:46 2008 +0000

    use the new compare tool

Tools/C_util/regtests/Castro-tests.ini

commit 8bad1c0d01ca12e37fda339917fa20796a6f7988
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:32:45 2008 +0000

    do the cvs update on fParallel still

Tools/C_util/regtests/test.py

commit 1ba055073c489de67df919596323f0b020cd4c65
Author: mzingale <mzingale>
Date:   Mon Jul 21 19:28:27 2008 +0000

    new compare tool

Tools/C_util/regtests/Maestro-tests.ini

commit 06d566d5d7ca8e7c3c6da2df940f32c8971709d0
Author: mzingale <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 af86adf04d5b329540c1dffcb83b19dfe28bf03a
Author: almgren <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 3377bdc8e2b69342bcf072fa1927bdcfaff686b5
Author: almgren <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 5cf07700120338b376e2e9696d503f4c37e59b2b
Author: ajnonaka <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 c9017bd391716ebacc81a4280af8239096f5baf0
Author: marc <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 037141b3444c5386fd6731a41558b5e4f5a431e3
Author: almgren <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 12d640b569f9e122b123a8f0c7f2862a21be2eca
Author: almgren <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 847dc590773bc04110e6ebc49506acbbe265bf3b
Author: lijewski <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 251b35b2fa7f9f7bd184c64361d3c9b0a224f16e
Author: lijewski <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 0e0589f4f8876fb5ce5e9cf5fed20640ab0107d1
Author: lijewski <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 2063b6c2bdc82d3d9641294cef8a0f46977a07e1
Author: lijewski <lijewski>
Date:   Sat Jul 12 18:51:45 2008 +0000

    plugged memory leak found by Candace

Src/LinearSolvers/F_MG/mg.f90

commit c1e8efa227ea422041f796c14b8aae34e4a85049
Author: lijewski <lijewski>
Date:   Thu Jul 10 23:24:16 2008 +0000

    removed unneeded module usage

Src/F_BaseLib/make_new_grids.f90

commit ae249cc2ce280dfd3997721d012788e0c7b6c571
Author: lijewski <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 98021f6e5906dba352ca7eda32c6449e0b04eb17
Author: lijewski <lijewski>
Date:   Thu Jul 10 20:08:47 2008 +0000

    added a TODO and a timer

Src/F_BaseLib/cluster.f90

commit bd2e762896895214ffadab2386e30dcaad1f9db2
Author: almgren <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 1be84475559e1a3d3d8f6dd2fed264f1e7383c1b
Author: almgren <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 b19447ab62efeee12d7c090823cc838512a00587
Author: lijewski <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 ebc88405e4748164f550556db6999b8b1fca878f
Author: lijewski <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 7513a6e4442b2c19f20a7e86d0ab4e5b9918596e
Author: mzingale <mzingale>
Date:   Thu Jul 10 17:12:32 2008 +0000

    get this working for fParallel runs again

Tools/C_util/regtests/test.py

commit d52b95acddb45489b89b528ac3087a8a34743b2b
Author: mzingale <mzingale>
Date:   Thu Jul 10 16:55:57 2008 +0000

    document the MPI stuff

Tools/C_util/regtests/test.py

commit 491b3f02ad53cf5eabc1e2c830cb762b6caaa023
Author: lijewski <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 f1f0c573eb6f1e038313cbdcecc10d91b4255cc9
Author: mzingale <mzingale>
Date:   Thu Jul 10 14:21:17 2008 +0000

    add parallel:

Tools/C_util/regtests/Castro-tests.ini

commit b5972f65a1b27fd16ddd09369ede3773683ccd0d
Author: mzingale <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 ea1193bff9a7dba3dee15944b5416eb71c9decc2
Author: mzingale <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 a622089a2976aa2e4fa860f34647d0de10b8e0aa
Author: lijewski <lijewski>
Date:   Thu Jul 10 05:57:52 2008 +0000

    removed couple unused & broken routines

Src/F_BaseLib/boxarray.f90

commit 715c9f0a8a672d60c86505f3636e77c83cccabc0
Author: almgren <almgren>
Date:   Thu Jul 10 01:25:37 2008 +0000

    Fixed subroutine buffer.

Src/F_BaseLib/make_new_grids.f90

commit d8530bbe1ef0c958bc939a94408c5dca036cbc8a
Author: almgren <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 2c20a24e108512c9036f55dc97bdb432d5677167
Author: almgren <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 95b464619fa404072bc5102b339a565dc8b69632
Author: almgren <almgren>
Date:   Wed Jul 9 22:28:57 2008 +0000

    Add machines manda and DELLA as new options.

Tools/C_mk/Make.mpi

commit 481627e08cdb0fedfdd2b48b674d9c3abc96fb07
Author: lijewski <lijewski>
Date:   Wed Jul 9 20:16:26 2008 +0000

    some cleanup & memory leak squashing

Src/F_BaseLib/make_new_grids.f90

commit 6c7419f183850bfc9870d86047f0b5f9285d9640
Author: lijewski <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 00aa749d29306d68d344bb7a3bed95586214dd10
Author: almgren <almgren>
Date:   Wed Jul 9 00:04:58 2008 +0000

    Renamed regrid.f90 --> make_new_grids.f90

Src/F_BaseLib/make_new_grids.f90
Src/F_BaseLib/regrid.f90

commit a19cba9792fa81be52d72d66fa8271ee338b9c21
Author: almgren <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 438704d400645df6ac1448c434bae5cc5540a038
Author: almgren <almgren>
Date:   Tue Jul 8 23:39:52 2008 +0000

    Remove commented line.

Src/F_BaseLib/boxarray.f90

commit 3f3cbdfa1838d334e830b46ad97a5082855dce08
Author: lijewski <lijewski>
Date:   Tue Jul 8 23:08:13 2008 +0000

    tiny bit of cleanup

Src/F_BaseLib/multifab.f90

commit ca428d39938f2c068f38d4e2df7b835f4912ede1
Author: lijewski <lijewski>
Date:   Tue Jul 8 21:54:12 2008 +0000

    first cut at map_periodic()

Src/F_BaseLib/cluster.f90

commit 35ecf29d2b844be0aa262f988e5fa22bbd23eaf3
Author: almgren <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 b47b24bc9e56532b646a6239982a1c79c66ace06
Author: almgren <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 401a1a39db95bf510b0fde14672677ccb532f750
Author: almgren <almgren>
Date:   Thu Jul 3 00:05:28 2008 +0000

    Add another sanity check for proper nesting.

Src/F_BaseLib/ml_boxarray.f90

commit 8f285f7e5310ab83d99380a3112192093ea7e325
Author: almgren <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 8ceda966e24088e551717c2fa67db8348a4baec3
Author: almgren <almgren>
Date:   Wed Jul 2 23:15:57 2008 +0000

    Removed commented line.

Src/F_BaseLib/fabio.f90

commit ea6dcd424043fe0e03b2c15db58cdefe384e2d8a
Author: almgren <almgren>
Date:   Wed Jul 2 22:52:15 2008 +0000

    Fix ml_layout_restricted_build.

Src/F_BaseLib/ml_layout.f90

commit cc486a1540e3847d1791562dfe407ba5e692852b
Author: almgren <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 c036f1908bfc01ae875165ce52f6b3b8aae64a12
Author: ajnonaka <ajnonaka>
Date:   Wed Jul 2 16:13:31 2008 +0000

    plugged a very sneaky memory leak

Src/LinearSolvers/F_MG/mg.f90

commit 0b271da925658dfa748047bd7a91bff2706963d6
Author: lijewski <lijewski>
Date:   Tue Jul 1 18:00:10 2008 +0000

    now contains GetBndryCells()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 0537ac8a7f98d77821b31f63337dee94110732ec
Author: lijewski <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 21f750c45b9a5ae3a0940ccb9b79eeb8c969d2d1
Author: lijewski <lijewski>
Date:   Mon Jun 30 22:05:03 2008 +0000

    minimize copy()ing

Src/F_BaseLib/multifab_fill_ghost_cells.f90

commit cbe2fdfed5874a1732578d421fe31b4a7b4cbde5
Author: lijewski <lijewski>
Date:   Thu Jun 26 23:04:34 2008 +0000

    slight reworking of ml_boxarray_properly_nested()

Src/F_BaseLib/ml_boxarray.f90

commit 5a67691aeb1c7b9a488b7d4be05c15401651c9cd
Author: lijewski <lijewski>
Date:   Thu Jun 26 21:02:48 2008 +0000

    more efficient periodic tests in properly_nested()

Src/F_BaseLib/ml_boxarray.f90

commit eb7de21cf3417eae17a54cc8d35a655fd294096a
Author: lijewski <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 b38d8a0306816ea59303cd7ad7d5988f6982788b
Author: lijewski <lijewski>
Date:   Thu Jun 26 15:58:19 2008 +0000

    *** empty log message ***

Src/F_BaseLib/boxarray.f90

commit 61fa51333ce5e72ff6d790c28079d8b483f64276
Author: lijewski <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 32a4e9ce3bf754a132291aee67712eba80cf7cd0
Author: almgren <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 bf654d4188b3742cbef23f43221443385949f9cb
Author: ajnonaka <ajnonaka>
Date:   Thu Jun 26 03:51:35 2008 +0000

    added "use_bl_error_module".  Code compiles again.

Src/F_BaseLib/boxarray.f90

commit 72b801590e3819401b683df119759b83afd4e776
Author: almgren <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 1bf25b6685afcdd82d5784b64f20993df67ede95
Author: almgren <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 d3d32346454aa95feb74c2c98eff973aa2bfe351
Author: almgren <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 ca0badbff30c4bc77af6814ccabb25607970e33c
Author: almgren <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 2e696263f83b32cd9e721094ca2005318b3012b1
Author: almgren <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 73f7d020101471e7cb5bd3d18dc1a325dd0bb29d
Author: lijewski <lijewski>
Date:   Wed Jun 25 17:25:51 2008 +0000

    some cleanup

Src/F_BaseLib/cluster.f90

commit 7007010538cd7bf3435a1f4e71eb8c82dfaa6e17
Author: almgren <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 b53c15ade4793c3da874f53be0f8ce9f30238bb5
Author: almgren <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 31cced15781a353d85a0e66ddbd8715487164b77
Author: lijewski <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 b54676384b38813cb188e0a33fe72ac3c079c41c
Author: almgren <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 d2a8c3176c5e80b88a9a6e4f9a40024ad8dbb9e3
Author: almgren <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 f33bd47fea847b82e8332c7e5d7693b2130d9bcc
Author: almgren <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 37c916862c61966b3dc2d332a31d39df27ac3a59
Author: almgren <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 ab0b08e63567acab10babfe490f893fcd2c817d3
Author: almgren <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 a62fe8c2ee4ab5190a58697ddc28c4ca543ec0e4
Author: lijewski <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 5e798361b32ff9d6512df8f76cd43be990829e86
Author: almgren <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 a1dffa108bc48d9c8bd45972f9b644c653dcddb7
Author: lijewski <lijewski>
Date:   Mon Jun 23 21:29:27 2008 +0000

    removed potentially troublesome where constructs

Src/F_BaseLib/box.f90

commit 9fc44c6ea8e623ce63aca305486c2124faa8d6cf
Author: ajnonaka <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 7adbf45eb1e95c58a350c2566ccb3a97f2dd399b
Author: ajnonaka <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 901802abe9558533736f07dc1c72995e8a904784
Author: lijewski <lijewski>
Date:   Sun Jun 22 18:02:27 2008 +0000

    *** empty log message ***

Src/F_BaseLib/cluster.f90

commit 50990ab23dc1204f4d0b1b7e731c9a5f88ea654d
Author: lijewski <lijewski>
Date:   Fri Jun 20 16:34:52 2008 +0000

    clustering now works in parallel

Src/F_BaseLib/cluster.f90

commit c84e14abf774563699f944eb214ffb85d8f17553
Author: lijewski <lijewski>
Date:   Fri Jun 20 16:33:50 2008 +0000

    changed verbosity defaults

Src/F_BaseLib/knapsack.f90

commit dbe8d247e12318dc4938fd6fa474aa88bb861f14
Author: lijewski <lijewski>
Date:   Mon Jun 16 20:50:56 2008 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 3bf2525f291e3ce77ed228aa00a6f02c7382142c
Author: lijewski <lijewski>
Date:   Mon Jun 16 17:46:12 2008 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/ml_restriction.f90

commit da2f87a30f0a4b9e42751e422a808349ebd315ce
Author: almgren <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 29f27a7f678e594cac96b38ab02909559a470ab5
Author: almgren <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 c255b90544bce85865a0d714a3dd59c25a473785
Author: almgren <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 8f34f1ef302c56196e91b69083f6288d49fdc898
Author: lijewski <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 04376972f6a837c443579df5cbdeb91e7c22d877
Author: mzingale <mzingale>
Date:   Mon Jun 9 23:50:40 2008 +0000

    fix a model file

Tools/C_util/regtests/Maestro-tests.ini

commit e692b0458101d477949c99dfb08bb1bb121c50de
Author: almgren <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 fb80ba863a94656ed8e8b26c297d61ed01386a64
Author: mzingale <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 f79d558559bd400fb348a88fc6d06d6cb896734a
Author: lijewski <lijewski>
Date:   Tue Jun 3 23:45:09 2008 +0000

    some simplification of VisMF::Write

Src/C_BaseLib/VisMF.cpp

commit 07e15d44487a86c182d2ca089ea9237c8b883f91
Author: aaspden <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 b64099265853ec4bed4cb95b23c11d7909b3930b
Author: almgren <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 da858ea952627d65565ba01cda0ff472e2944385
Author: almgren <almgren>
Date:   Tue Jun 3 19:44:00 2008 +0000

    Change la to "in" from "inout"

Src/F_BaseLib/bndry_reg.f90

commit 32621f64d255a01a5d7a11b2a14a33114a9d7a55
Author: mzingale <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 cab9baaf7a906de3fa47cf8a53cd76d299be49cd
Author: jbb <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 ce822fd42bc61cc9913a68c2e798ddb53ce286b9
Author: gpau <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 a44300a6d0e4a0bdd56c7fcbc05ab97e357a299c
Author: lijewski <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 0a6635c7ef218e89d5bbf55ff2bc30588d1a79bf
Author: lijewski <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 6e9811b20ce1caa22605c92bf6ce93edc89e8196
Author: mzingale <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 f1f36538fb2789e095c625e5a55ac8a755123d34
Author: mzingale <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 d7620debf0e64e0e101b205a18c6abf0e5c6740f
Author: lijewski <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 b2435464f5b4c6466f43668b68eb4156889953e5
Author: almgren <almgren>
Date:   Fri May 9 17:28:58 2008 +0000

    Remove unneeded variables.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 8178539b07346703ed87ff6e007a717e609ad88c
Author: almgren <almgren>
Date:   Fri May 9 17:26:17 2008 +0000

    Small code cleanup.

Src/LinearSolvers/F_MG/stencil.f90

commit 571e96ee03bae9456afe06faed203000c44ff2f8
Author: almgren <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 521c1d3e23aea836945331bf49877de5953ff6b4
Author: almgren <almgren>
Date:   Wed May 7 20:19:34 2008 +0000

    Removed unneeded "lenx".

Src/C_AMRLib/FLUXREG_1D.F

commit a0a4993c63fa04a890111a526dad8c57069eb0f9
Author: almgren <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 4d1adefb266489029795c15aee83ec149daca4b6
Author: almgren <almgren>
Date:   Fri Apr 25 20:45:49 2008 +0000

    Can't use 0.d0

Src/C_BaseLib/MultiFab.cpp

commit 223014f0386233cf38ae0b5c8058424635fdc3fb
Author: almgren <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 875ae127bddc67ff5940d9a65f708b40ce713b5f
Author: lijewski <lijewski>
Date:   Mon Apr 21 20:02:00 2008 +0000

    added build_random_boxarray to public interface

Src/F_BaseLib/mt19937ar.f90

commit bd8dfaa9635e648ab6b0c3f5849ecbf12ee96862
Author: lijewski <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 4d2d6a7ed72bf83f6b78844f8a662caacc1df1f9
Author: aaspden <aaspden>
Date:   Thu Apr 17 23:10:54 2008 +0000

    Gimantis update

Tools/C_mk/Make.defs

commit f0e5708f89b5601064b54f7f742176407115f6db
Author: mzingale <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 4ec073a566408de1421d699db6fe0a767a4ca860
Author: mzingale <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 d92c901531c1d46f8237d1933b1f240cb79a67fc
Author: mzingale <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 1075a9f3dd51a04360f998a9b8d79161f9ee44e4
Author: almgren <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 1720acacb6752504e7d4d702f300814c0d21a6e0
Author: almgren <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 a149483935db93818944a2cb50b79ef2c3aa5c11
Author: lijewski <lijewski>
Date:   Thu Apr 10 21:14:48 2008 +0000

    now print out # CPUs MPI initialized with

Src/C_BaseLib/BoxLib.cpp

commit 92783452f235b19c9d2d16f77c3f90f2fb844766
Author: almgren <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 933c3b4686f5ec6edf795ff72f7b9d7ce41b603e
Author: almgren <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 13f27ad7d4a0478064c23690bd0a59d0fd3500b6
Author: ajnonaka <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 223ce1062ebd94aca9a4a1bf56f5099a9ca637ea
Author: lijewski <lijewski>
Date:   Wed Apr 2 20:39:43 2008 +0000

    modest touch-up to norm0()

Src/C_BaseLib/MultiFab.cpp

commit de0f714f34d91ddb6127011ff178c693e7e7dec6
Author: almgren <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 24e40c47a947bbf12c0276c3fc2b6e7d211cc847
Author: almgren <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 3c2fed79cf9dd04e04bd516620272aaec5f9a53b
Author: almgren <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 4ae48b41428784f54870ad15262f910986a97adf
Author: vince <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 2bf3deaeec624e2172488a5e3273a1c2a32a7c09
Author: vince <vince>
Date:   Fri Mar 21 22:07:37 2008 +0000

    i/o fix.

Src/C_BaseLib/RealBox.cpp

commit 21027fb55efcd7cdc083eba2b073dbfe3961d5f4
Author: almgren <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 be0ab32a17d8255c5d4a6329998a64d45a7ebbfb
Author: almgren <almgren>
Date:   Tue Mar 18 19:54:35 2008 +0000

    Candace found missing destroy -- fixed here.

Src/F_BaseLib/cluster.f90

commit aa36af7f1e4d89c57689dae1007c55f6890d67e1
Author: jbb <jbb>
Date:   Sat Mar 8 00:56:53 2008 +0000

    added mpi link for gimantis

Tools/F_mk/GMakeMPI.mak

commit 8cd11b1d05c26ca1dbad890e096922172aada956
Author: mzingale <mzingale>
Date:   Tue Mar 4 20:03:12 2008 +0000

    fix jaguar compiling -- now it handles modules correctly.

Tools/F_mk/GMakeMPI.mak

commit 2146ec424b5bf42bc540888091ab75b0457ddeab
Author: lijewski <lijewski>
Date:   Tue Mar 4 18:41:19 2008 +0000

    removed some profilers

Src/F_BaseLib/multifab.f90

commit cae88ed3c1ce767fca48f2ced0392c3906c1cfa6
Author: ajnonaka <ajnonaka>
Date:   Mon Mar 3 22:07:23 2008 +0000

    fixed a comment

Src/LinearSolvers/F_MG/ml_nd.f90

commit 90cfd64598321a73cea95c032295c1fedaa30b2c
Author: mzingale <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 27bdbb22ad9cb235a918bffbbd93ab9fb77f13d6
Author: almgren <almgren>
Date:   Mon Mar 3 18:03:07 2008 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f9308ace521793abc4ab32f1bc90050c5fcf20ee
Author: jbb <jbb>
Date:   Mon Mar 3 17:38:15 2008 +0000

    Add case for mothra.

Tools/F_mk/GMakeMPI.mak

commit a81132814c99a6310bb76d97e289f259600a060a
Author: almgren <almgren>
Date:   Mon Mar 3 03:13:43 2008 +0000

    Add subtract_divu_from_rh.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit 0024c0fe9f29d74fcb248866d2c4cdecc39467d0
Author: almgren <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 277ff1ba980a840edee5e4b52e9e724d3bc58265
Author: almgren <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 893dad3ad0de0f45a479b44d31a8591112b91896
Author: lijewski <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 f7ca39fec6ddb03df7fdeeafc429eedd43a15fa2
Author: jbb <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 e6fd00ce25408e1f62ac452770056a02d2eb7ff6
Author: ajnonaka <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 53e6bc6c9b0853095a2f99fabf8072a8caaf00cb
Author: ajnonaka <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 ab16652a0d5552b0113fe6cd0e106136dd38dff9
Author: ajnonaka <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 12173650b29ea646adce19099f9ac1cacbb3cd9d
Author: ajnonaka <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 a46f716ae57a571ccc0384b88ba305888a3d43b3
Author: ajnonaka <ajnonaka>
Date:   Thu Feb 21 21:06:52 2008 +0000

    works for jaguar now

Tools/F_mk/GMakeMPI.mak

commit f89ec7c26876e68822b86798c3100734a0e62d0b
Author: almgren <almgren>
Date:   Thu Feb 21 18:44:50 2008 +0000

    Add "all = .true." to setval for buf.

Src/F_BaseLib/cluster.f90

commit fb9dbea5abfe1e1a71d251cdf82ae2cd1cd8ba29
Author: almgren <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 c9deccf397b7649e3df6ff3f6c7a01f35832605f
Author: mzingale <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 b5e4f7da4963601e4da9fa8567e9cf8d80911109
Author: vince <vince>
Date:   Wed Feb 13 21:24:57 2008 +0000

    more gimantis additions.

Tools/C_mk/Make.defs

commit 40c3570a6b2105cdf637fb9e7ef5b5de60fa688c
Author: vince <vince>
Date:   Mon Feb 11 23:54:22 2008 +0000

    additions for gimantis.

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 3c17ab3146a26d8a0162c2ba9f8da6292233e596
Author: marc <marc>
Date:   Fri Feb 8 20:56:10 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 7b982b7c14872b00c184d663c5bedcb49f44e46e
Author: jbb <jbb>
Date:   Fri Feb 8 20:22:31 2008 +0000

    make mothra work

Tools/C_mk/Make.defs
Tools/C_mk/Make.mpi

commit 0685351c868453936970e03fb491dc685da65acb
Author: lijewski <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 c19691b1b16a5cbcb14804cfcddeae1584b86e15
Author: lijewski <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 18e3d0d6fcf82a5b3e962dba297c86ddc364f8d8
Author: lijewski <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 906e5b19700e3c3688416d081016d042b490e2a6
Author: lijewski <lijewski>
Date:   Thu Feb 7 23:48:08 2008 +0000

    some cleanup

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit ddd8b331ebdc6b2b55c1cd1f57690390e8bdfaa6
Author: lijewski <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 decfd04f09a11335fd3ea9e96b59f8c1985f0a02
Author: lijewski <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 fba3c4a450447864a660d6989ab7dd27a91eeea0
Author: lijewski <lijewski>
Date:   Tue Feb 5 20:05:00 2008 +0000

    added -mp for Intel 9/10 optimization

Tools/F_mk/GMakedefs.mak

commit e1e3823a49f9e816ff0f23168a7c63873cbdfef9
Author: ajnonaka <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 8b41a4ff4c2a23ee52c664dac3b5eba8a9fffad3
Author: sepp <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 6ffb73f6c25e9703a775a0316d8cca259b5094b6
Author: almgren <almgren>
Date:   Thu Jan 31 21:51:03 2008 +0000

    Added options to make mpi work on pleiades.

Tools/C_mk/Make.mpi

commit 20e82626b818314181ca23819a1d46f2c57059f7
Author: marc <marc>
Date:   Thu Jan 31 18:58:36 2008 +0000

    += instead of =

Tools/C_mk/Make.Linux

commit 843a8e3c2a57eabd44bac6fd0bc2b14347d51a08
Author: marc <marc>
Date:   Thu Jan 31 18:50:17 2008 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/Make.package

commit c40af9d17590bc866ef4a429a7b29aee290b35ff
Author: lijewski <lijewski>
Date:   Thu Jan 31 18:31:02 2008 +0000

    more IO wraps

Src/F_BaseLib/multifab.f90

commit 6d4e2872fb7ff881ad1ef9682249f0dc60d4e65a
Author: lijewski <lijewski>
Date:   Thu Jan 31 18:25:46 2008 +0000

    parallel_IOProcessor() wraps in print()

Src/F_BaseLib/multifab.f90

commit 0f60c9785f63968b85ba259c5fac50e525906234
Author: marc <marc>
Date:   Thu Jan 31 18:20:54 2008 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 21b3f84f095bd4adaaf37503b43dc2d2e576a8a7
Author: almgren <almgren>
Date:   Tue Jan 29 17:56:49 2008 +0000

    Fix misspelling in command line option.

Tools/C_mk/Make.defs

commit 6432cb647126991163981aaf154ed50f2991198d
Author: lijewski <lijewski>
Date:   Mon Jan 28 20:42:10 2008 +0000

    added profiler to ml_nodal_restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 9ed3251d1c861771d2dbfea67715e2ee0e087543
Author: lijewski <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 c3306ac5420115bde33ef0a5741af7af6a4fc0b5
Author: gpau <gpau>
Date:   Thu Jan 24 23:54:18 2008 +0000

    PathScale bug fix

Tools/C_mk/Make.Linux

commit b1c77f2432b44dea21d77092f3db3b71259af00f
Author: mzingale <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 d73d3a8e12ef3b7902094f45de474fccad2304fb
Author: mzingale <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 533d0280c5c86f2ec0df3b7e6c144b98bbcd1304
Author: lijewski <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 44d33cb58ccd6511066bfb2ddf477030c17149dc
Author: lijewski <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 e1bb6ffc5a953e013570403d2d45cf32a5232656
Author: lijewski <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 ae4f9c8cdcd391c417dbda2c3078882b5836164c
Author: lijewski <lijewski>
Date:   Wed Jan 23 20:39:13 2008 +0000

    couple very modest optimizations

Src/LinearSolvers/F_MG/mg_smoother.f90

commit d72b97fe17d38dbbb0e9d36bb39b97ae046ff8c0
Author: lijewski <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 b6dce4c06a41ad928c32136df9dcc3ff3e31dabb
Author: lijewski <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 6be7a2e2c5b56bb8264ad4766b5f3befa42d10ec
Author: lijewski <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 494fa4095417fb06df64334f304389562fcd8dfc
Author: mzingale <mzingale>
Date:   Sun Jan 20 21:46:03 2008 +0000

    add compilation rules for homer

Tools/F_mk/GMakedefs.mak

commit 69af824cbdfe7ea24ec43b6efabe6466486cd6ae
Author: lijewski <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 c2c4b2b9988c8926fe051b48b0d11e19684739af
Author: mzingale <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 9fffcf1dfde6febb6474a7ea58a8a6aceff3ed8e
Author: mzingale <mzingale>
Date:   Tue Jan 15 22:53:40 2008 +0000

    add support for Intel 10.1

Tools/C_mk/Make.defs

commit b25708eaa702a4df8531b7f0eb0048dc862190bf
Author: ajnonaka <ajnonaka>
Date:   Tue Jan 15 22:01:38 2008 +0000

    changed PathScale compiler options to -O2 -ipa

Tools/F_mk/GMakedefs.mak

commit e73a813edac38e1107848fe84753e7e8adf1cb1d
Author: almgren <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 3a1094c53684355c9a64e19e0458f00f0d934c97
Author: almgren <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 0fa597028c7b0ed8bcf84430cd3f20b9085a68ce
Author: almgren <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 9f54aeea4f10ca3f768caab9efca6eecfde3681c
Author: almgren <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 23a4a1e45a044a65032f672f6a3b4a1355f3d12c
Author: lijewski <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 cc4efff576087dc68891d5ae6972cfbd38de14d3
Author: lijewski <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 c20e1721c14935bc0c2bbf5ce6dd5b9354b67d99
Author: lijewski <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 d2a38d27ae9c1d1f3e01c33c393ac1505ff776b6
Author: lijewski <lijewski>
Date:   Mon Jan 14 20:06:38 2008 +0000

    obmf multifabs are now build optionally

Src/F_BaseLib/bndry_reg.f90

commit abbf6c4652c9d3e678b1c87443bb542ab1011e86
Author: lijewski <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 77b9fa9af787819e1181d7b13bb8280002cf2710
Author: lijewski <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 ed2553d94e96721d2c8295bb58ee4fc0f4ba77e7
Author: lijewski <lijewski>
Date:   Sat Jan 12 04:44:21 2008 +0000

    fixed parallel bug in bndry_reg_build()

Src/F_BaseLib/bndry_reg.f90

commit 942ed36e7141438651dca5459969ef127e69a8fc
Author: lijewski <lijewski>
Date:   Fri Jan 11 22:52:28 2008 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90

commit 6f276a40c651ccf23df4d2c8d9f5b1b7549a661c
Author: lijewski <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 8e37b6081cc4ff106dde8f4a4f730d99225ab55f
Author: lijewski <lijewski>
Date:   Fri Jan 11 22:29:36 2008 +0000

    added least_used_cpus()

Src/F_BaseLib/fab.f90

commit 4bebbd7ae67e30c1095fc92f5ae2cd331c2dd541
Author: lijewski <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 1c1b24fe29a6e30e4e14333427b4c22240061fa0
Author: mzingale <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 fa1518bd7206be6894ba97321d80692a4376250f
Author: mzingale <mzingale>
Date:   Mon Jan 7 21:13:27 2008 +0000

    enable bounds checking for gfortran

Tools/F_mk/GMakedefs.mak

commit 000be82c45646cc79124fed04fba71c74d8009e3
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:44:21 2008 +0000

    fabs no longer have an ng component

Src/LinearSolvers/F_MG/stencil.f90

commit 5a6e671c4b40fe2f9a381fdf650261e875d9e730
Author: lijewski <lijewski>
Date:   Thu Jan 3 23:43:59 2008 +0000

    Removed multifab_debug_fill().

Src/F_BaseLib/multifab.f90

commit e4ebb2e4cb3369644b030ae137596b2b0b72c1fa
Author: lijewski <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 9c78de614b5918cf5466798a777725d2e62ea4fa
Author: lijewski <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 1a595143b4ef41f9796fae7ccca3d117f60caabd
Author: lijewski <lijewski>
Date:   Thu Jan 3 06:11:53 2008 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90

commit 1bfc5fcfc324bf900b560df821e7c3588131965b
Author: lijewski <lijewski>
Date:   Thu Jan 3 05:35:29 2008 +0000

    code for calculating & printing fab byte spread

Src/F_BaseLib/fab.f90

commit 48259b091b249bca65721a50234934e71ad7b899
Author: lijewski <lijewski>
Date:   Tue Jan 1 21:04:37 2008 +0000

    fixed more parallel bugs

Src/LinearSolvers/F_MG/itsol.f90

commit b75a8fc72188ac09f5aba2878b59684d213290fe
Author: lijewski <lijewski>
Date:   Tue Jan 1 17:15:53 2008 +0000

    added aveassoc stuff

Src/F_BaseLib/layout.f90

commit 2d35dd6b75df6d4c368f58aa12df0c052fdf19de
Author: lijewski <lijewski>
Date:   Tue Jan 1 16:28:45 2008 +0000

    added sort_i.f90

Src/F_BaseLib/GPackage.mak

commit fd6eabdef1316399760e93ad0c84d027c9f8e0a5
Author: mzingale <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 90b08a5c5b9c9fd45d6b2cc6bb86a8aad4ae4306
Author: lijewski <lijewski>
Date:   Sat Dec 29 04:13:52 2007 +0000

    removed the bound member -- not used

Src/F_BaseLib/multifab.f90

commit d46a9ee98ec0233c3f5854ce2cb480be0482e3dd
Author: lijewski <lijewski>
Date:   Wed Dec 26 20:32:02 2007 +0000

    more mem_stat refinement

Src/F_BaseLib/fab.f90

commit 2e36895a1728131ca5d3f268f406562b0c864bb1
Author: lijewski <lijewski>
Date:   Wed Dec 26 19:49:18 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit e0284c83bc9624db57a6ed8d767cbc9bf7a79135
Author: lijewski <lijewski>
Date:   Wed Dec 26 19:32:31 2007 +0000

    more work on mem_stats for cached data

Src/F_BaseLib/layout.f90

commit 893e7415daadeaf259dd7e577ccb68ebae47d551
Author: lijewski <lijewski>
Date:   Wed Dec 26 02:25:05 2007 +0000

    more mem_stats stuff

Src/F_BaseLib/layout.f90

commit 46787417ee2114ec0bab0f506c30a69bbbcea681
Author: lijewski <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 80f65a0b11d567234d0d9e34b8adfeba51039656
Author: almgren <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 4b3ef2f0807997b4b5eec42460783ceacb29a0ab
Author: lijewski <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 071dcfc581c30b8d7916098926ebbc708f629a3c
Author: lijewski <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 80009724202022339b20cf48a328025ddaacbb5f
Author: lijewski <lijewski>
Date:   Mon Dec 24 20:36:34 2007 +0000

    run boxarray_maxsize() on boxarray stored in fgassoc

Src/F_BaseLib/layout.f90

commit cdd0b938a1c1bd701c3c2f61e7b6c11454cd20d1
Author: lijewski <lijewski>
Date:   Mon Dec 24 18:09:48 2007 +0000

    removed unimplemented routine

Src/F_BaseLib/list_box.f90

commit 998d2cbe913d52b46f0afa16c4e7c57d0e495064
Author: lijewski <lijewski>
Date:   Mon Dec 24 18:09:23 2007 +0000

    stop -> bl_error() calls

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit ccbf0a26652ca325032ab4c90b972c5f3afc2b04
Author: lijewski <lijewski>
Date:   Mon Dec 24 06:41:46 2007 +0000

    wrapped some output in parallel_ioprocessor()

Src/LinearSolvers/F_MG/mg.f90

commit f1390a06124fc1dfaf5fafcc8fde6ea768b5ac23
Author: lijewski <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 ce060f8427ba4a6e06c6ea0e9b5e753f90a0589a
Author: lijewski <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 0cd256cced28a2c1fa742cb32a003fe16214cbf2
Author: lijewski <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 398e64c6c3e2763b710d1f9a942f012653f74cf8
Author: lijewski <lijewski>
Date:   Fri Dec 21 17:26:29 2007 +0000

    moved from varden/MAESTRO directories

Src/LinearSolvers/F_MG/ml_solve.f90

commit 7b483de27d3be2d9cc3e5ca8ad3381cff4695638
Author: almgren <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 cc1ac02b7631c9333f790b07662b14638e958365
Author: lijewski <lijewski>
Date:   Wed Dec 19 20:42:10 2007 +0000

    needed bl_constants_module

Src/LinearSolvers/F_MG/nodal_newu.f90

commit d107891b92d4ee0f338a1272d8512a98ed9ca29a
Author: lijewski <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 44c68d4afdea8d28b93214c549d49e05b2193511
Author: lijewski <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 9b494b50ff53258db67c21223e27cfbaea6abddb
Author: lijewski <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 ad67d7bc8ed11a736a6ca4a5dddffa9d2426fa82
Author: lijewski <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 64e75777491acdd6ea72a018700a5aa8ed90ff2b
Author: lijewski <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 12e76f3e5070a58086b9737c0f7a7bb53e97c11e
Author: lijewski <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 de2878967470594fbf20a2471b9ca349c322ddf1
Author: lijewski <lijewski>
Date:   Tue Dec 18 17:40:05 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit fe0cba25695baad37787885cea8e9c19db526406
Author: lijewski <lijewski>
Date:   Tue Dec 18 17:24:37 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 6b790f13e2a846bb1aff728d37ca4feb520a1a14
Author: lijewski <lijewski>
Date:   Tue Dec 18 00:22:47 2007 +0000

    fixed test in internal_sync_unique_cover()

Src/F_BaseLib/layout.f90

commit 2334fb99bbfe1c54684b37eaf5833fc6f9188d1b
Author: lijewski <lijewski>
Date:   Mon Dec 17 23:10:53 2007 +0000

    fixed bug in boxarray_same_q()

Src/F_BaseLib/boxarray.f90

commit b86096ce2e424b8550df295b8739729d0c912073
Author: lijewski <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 fb90da12211d28cee4916ad2e2d840f3c203136f
Author: lijewski <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 1686d5da257d4b579fc9aa9091a55d7f8415c2e5
Author: lijewski <lijewski>
Date:   Mon Dec 17 21:39:11 2007 +0000

    more cleanup

Src/F_BaseLib/boxarray.f90

commit 3ffb1869dba7657512087ad20aa8547dd3866c66
Author: lijewski <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 dadb70fcf9c75dfd1aeebdff800e004aa57bceb8
Author: lijewski <lijewski>
Date:   Mon Dec 17 19:11:40 2007 +0000

    removed some unused stuff

Src/F_BaseLib/boxarray.f90

commit 57ff637c2cc18408f2e85027ae5d162ea973100b
Author: lijewski <lijewski>
Date:   Mon Dec 17 18:24:07 2007 +0000

    cleanup & bug fix in boxarray_add_clean_boxes()

Src/F_BaseLib/boxarray.f90

commit 67a0cc903eb983a504538bcc38742ee04af4444d
Author: lijewski <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 8951ab4510b34a230685af4e1f08149bdacfbed9
Author: ajnonaka <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 20e59719b02c6dd65cd4b048bbdf5a1134b127ba
Author: ajnonaka <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 06333597977a55d064ba4d8918c4ed58977e7b93
Author: ajnonaka <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 7ff38b6455e3bc298c5a8fbd9dcc9b458ba3f0dd
Author: lijewski <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 fcf29f72afc8c6e311729bd07f1500e7a8ee12f3
Author: lijewski <lijewski>
Date:   Thu Dec 13 18:23:58 2007 +0000

    removed some profilers

Src/F_BaseLib/interp.f90

commit c0e74a010f23689eca87b57e7cd0fd0686432448
Author: lijewski <lijewski>
Date:   Wed Dec 12 20:28:07 2007 +0000

    added TODO note

Src/LinearSolvers/F_MG/nodal_divu.f90

commit f097679c4f88a96e081e1139061af8056196c7be
Author: lijewski <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 525ec2ecc55c212435d45d89b4f1502687faa8d4
Author: lijewski <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 f3d058be8132376ee68bd97c9a02a69862ecb72d
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:22:11 2007 +0000

    commented out unused norm_inf() call

Src/LinearSolvers/F_MG/mg.f90

commit ba91e36a432abd40ff4476af4ca22b8b255ba31a
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:21:30 2007 +0000

    added needed type casts

Src/F_BaseLib/mt19937ar.f90

commit f5c4d826dc0f9c6065ad823eb9b63c237e23bd3f
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:21:05 2007 +0000

    some type cleanup

Src/F_BaseLib/ml_boxarray.f90

commit bbe0967370ef2bf209a4c8fbd686981b3d0aeccd
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:20:44 2007 +0000

    some cleanup

Src/F_BaseLib/layout.f90

commit 338b6b79cf2865ae0072e0c4416101d54e35b4f2
Author: lijewski <lijewski>
Date:   Tue Dec 11 22:20:26 2007 +0000

    removed unused declaration

Src/F_BaseLib/fillpatch.f90

commit df4f2d143dc9b1aa5024894c0501a6e75a4223e8
Author: lijewski <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 a23802ab7a6c696e5b227f861cea6e4e54425167
Author: lijewski <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 3215fc2964c1f403a802400d0615cb5430d676ac
Author: lijewski <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 49ef743c84add4bace62c43f8f9467568420ef2d
Author: lijewski <lijewski>
Date:   Tue Dec 11 18:52:34 2007 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 5327bde909bb522a53120637b55a0c2fb7b021d7
Author: lijewski <lijewski>
Date:   Tue Dec 11 01:13:28 2007 +0000

    added some bl_prof timers

Src/F_BaseLib/knapsack.f90

commit 4ed60bb6f7e28eb364e60abf8ef93e8cee2a07e3
Author: lijewski <lijewski>
Date:   Tue Dec 11 01:01:23 2007 +0000

    added some bl_prof timers

Src/F_BaseLib/interp.f90

commit 3749ddebe90f1cf1d21cf9eb3a5161ec607f694d
Author: lijewski <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 d901ebb3a9b7570e04bd787592225bb413736b02
Author: lijewski <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 f4b27c609250f2382eb12bed5770671bb68b9d3d
Author: lijewski <lijewski>
Date:   Mon Dec 10 20:36:34 2007 +0000

    fixes to bl_prof usage

Src/LinearSolvers/F_MG/ml_cc.f90

commit 3d69944ef3b2f0d4ca16c25210115050bde6e66f
Author: lijewski <lijewski>
Date:   Mon Dec 10 18:59:56 2007 +0000

    parallelized ml_crse_divu_contrib

Src/LinearSolvers/F_MG/nodal_divu.f90

commit a3ff124ff5e9ddfabb38f747a72fb06879bbe382
Author: lijewski <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 fd9929b569f9721113c23d83071006db3364785b
Author: lijewski <lijewski>
Date:   Sun Dec 9 01:42:25 2007 +0000

    some cleanup

Src/F_BaseLib/box_util.f90
Src/F_BaseLib/fillpatch.f90

commit a9d05bef0d80ac43d52f1db6bd85b937360a20ef
Author: lijewski <lijewski>
Date:   Sun Dec 9 00:38:44 2007 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 893c39c2be080a92b265ec3f55f4947c5f73d83c
Author: almgren <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 b3fcf3fe4c37b5db8c9d718da1148895084d8d9e
Author: almgren <almgren>
Date:   Fri Dec 7 21:28:56 2007 +0000

    Put prototype regridding algorithm here.

Src/F_BaseLib/regrid.f90

commit ed3a447db19364c8335b7aa90e65f0f8442e89d9
Author: lijewski <lijewski>
Date:   Fri Dec 7 21:25:41 2007 +0000

    parallelized ml_interface_c()

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 4cf926313854038d0bdefa3a2ddd87589bfc969d
Author: ajnonaka <ajnonaka>
Date:   Fri Dec 7 19:58:14 2007 +0000

    mg test commit

Src/LinearSolvers/F_MG/GPackage.mak

commit d48121e84c4d74c3e9f238825988c72f667a4cb9
Author: lijewski <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 b4e12ae6910339907be15138f5b6af97f8d6f3ad
Author: almgren <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 40f7713210a466896c21d440e50dd1d14928230a
Author: almgren <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 0284ca40c17e18e176ad6cd9b93da3ec7a68d96c
Author: almgren <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 42dbd95c142060e6e23eca8591f9b99b318f893c
Author: almgren <almgren>
Date:   Thu Dec 6 20:39:40 2007 +0000

    formatting cleanup.

Src/LinearSolvers/F_MG/mg.f90

commit 401bc162e009192b3884edfe6bab50b8b0753f21
Author: almgren <almgren>
Date:   Thu Dec 6 20:39:25 2007 +0000

    Removed commented line.

Src/LinearSolvers/F_MG/ml_cc.f90

commit db2c11ac1cd247eb8128a10ec57ed4b905630f82
Author: almgren <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 0afddac083f560c24f07572cacac8ac60b7e4909
Author: almgren <almgren>
Date:   Thu Dec 6 20:38:04 2007 +0000

    Fix stuff in ml_prolongation.

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit bd1194fa3652240f46560bf119546067d7343770
Author: lijewski <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 a7e5e804960c842c61cfbbd50bd8ef623e24a747
Author: lijewski <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 a5a37e3f6eb4bc466f142420697b8817a39526f9
Author: almgren <almgren>
Date:   Wed Dec 5 19:00:27 2007 +0000

    Removed commented line.

Src/F_BaseLib/layout.f90

commit 45e79a6fdc5fd3ba6dd4a9dd522c6372afad5ad4
Author: almgren <almgren>
Date:   Wed Dec 5 18:36:21 2007 +0000

    Remove ng from bndry_reg_copy calls.

Src/F_BaseLib/bndry_reg.f90

commit 67a9bf6b64b9a7478f3df8493975c13f932b6ecb
Author: lijewski <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 01f671d6430d5da043a1925b214164ce841b3685
Author: lijewski <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 4c4e110c847bb8a970f33383ef818262f8923415
Author: lijewski <lijewski>
Date:   Tue Dec 4 23:48:40 2007 +0000

    some cleanup

Src/F_BaseLib/fillpatch.f90

commit 2b334505a45f882d3662727fb6e68f140b14e920
Author: lijewski <lijewski>
Date:   Tue Dec 4 23:39:37 2007 +0000

    plugged some memory leaks

Src/LinearSolvers/F_MG/ml_cc.f90

commit b744d21f8719287752e9104200d3a7ea519097fb
Author: lijewski <lijewski>
Date:   Tue Dec 4 22:56:18 2007 +0000

    bug fix -- only destroy fla & tmpfine if built

Src/F_BaseLib/fillpatch.f90

commit 5ddb5d87c8f18f6b6a5e7b5b6f847d3def24b6e0
Author: lijewski <lijewski>
Date:   Tue Dec 4 22:26:35 2007 +0000

    start on making fillpatch periodically-aware

Src/F_BaseLib/fillpatch.f90

commit 016624ef7ac8c370491af091e9491d3773e03dc2
Author: lijewski <lijewski>
Date:   Tue Dec 4 00:33:39 2007 +0000

    more error checking

Src/F_BaseLib/fillpatch.f90

commit 6f228ca90ca2e1fecc5b0b801de0d03206b5539e
Author: lijewski <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 bb0bd7beb2cef018c0fc5e03eccd7d09ced1afdb
Author: lijewski <lijewski>
Date:   Tue Dec 4 00:27:35 2007 +0000

    modest fixes -- still periodic issues

Src/F_BaseLib/fillpatch.f90

commit 99a521c4d62addad5d7b99d83914caf166ca1a61
Author: mzingale <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 1e8b22bad344c2503a2e5ca55fa3badb72b2e8f5
Author: lijewski <lijewski>
Date:   Mon Dec 3 22:18:48 2007 +0000

    modest bug fix

Src/F_BaseLib/fillpatch.f90

commit d3f9b2c7eff7352cbf6944eccbc67973d5a3edda
Author: lijewski <lijewski>
Date:   Mon Dec 3 17:37:30 2007 +0000

    mods from Mike Singer

Tools/C_mk/Make.mpi

commit c33d08a3aefaf3a511b65cf2a6b0334a2c6b7a1f
Author: lijewski <lijewski>
Date:   Mon Dec 3 17:28:39 2007 +0000

    mods from Mike Singer

Src/C_BoundaryLib/LO_BCTYPES.H

commit 61954f66502fa0c12e398d9a8c9fdefa8bedc5ec
Author: lijewski <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 725b1ba43522f365e15331e18d1bfc8e373870b9
Author: lijewski <lijewski>
Date:   Sat Dec 1 00:21:44 2007 +0000

    little cleanup

Src/F_BaseLib/fillpatch.f90

commit 5a4d113c149ac6dc1aaa653e52671ae375addd0c
Author: almgren <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 87dac27cf95bd9efa75ccb6e5cb039ca4a0fe1ef
Author: almgren <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 1c116d9a8afafe61f4845dae8b1fa94c7fec3726
Author: almgren <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 4a73c494e2d33f5dc353b02821b5c1e401416654
Author: almgren <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 69be5a43d8840b54e74271c3f673407bdd8bb8ed
Author: mzingale <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 d03247ad46cd393740c1c777d6f633d9106dd565
Author: mzingale <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 04441420aa37339581d32821e9d994f467fff04e
Author: ajnonaka <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 d62560be857affd7d607b16727e260c965e8ef50
Author: mzingale <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 2511da0a0a45821882398cff325166becf0ad68d
Author: ajnonaka <ajnonaka>
Date:   Sat Nov 17 01:53:49 2007 +0000

    cleaned up code for easier reading

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 3c366d29d301ab3356f29c5f542019a12613c156
Author: lijewski <lijewski>
Date:   Wed Nov 14 22:20:53 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 285097eb8da5ccd2f536003808eb28c617a97c04
Author: lijewski <lijewski>
Date:   Wed Nov 14 21:04:25 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 6b826b61cde333a457d0b64d4d0f81cec0ab50d1
Author: lijewski <lijewski>
Date:   Wed Nov 14 20:33:03 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 4f544fb2e733a09eca52bb171d123a1b69a5e97c
Author: lijewski <lijewski>
Date:   Wed Nov 14 18:42:15 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 64e33b0da48482aa9719c02ae0c208bc28c98e1f
Author: lijewski <lijewski>
Date:   Wed Nov 14 03:51:45 2007 +0000

    centralized PGI and PathScale stuff

Tools/C_mk/Make.Linux

commit 35125ec746decf875101490d73d30015cd19fcfb
Author: ajnonaka <ajnonaka>
Date:   Tue Nov 13 18:43:25 2007 +0000

    plugged a memory leak

Src/LinearSolvers/F_MG/ml_cc.f90

commit b05d74bcee80de2e495e2107bbe5e27c3c48b71d
Author: mzingale <mzingale>
Date:   Tue Nov 13 15:48:56 2007 +0000

    turn off debugging

Tools/C_util/regtests/test.py

commit 6e5c5e518273b59f046c996c8d20b8af1ebe325d
Author: mzingale <mzingale>
Date:   Tue Nov 13 15:01:34 2007 +0000

    add an entry for nan.astro.sunysb.edu

Tools/F_mk/GMakeMPI.mak

commit a73af2db3978cfec878157fcd7ca29e903d60b5a
Author: lijewski <lijewski>
Date:   Fri Nov 9 23:05:40 2007 +0000

    added some commented out options for Franklin

Tools/C_mk/Make.Linux

commit 970b41ee119fd42efdaa24c67cc78ec3a4f14389
Author: marc <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 3f9d06be34065691b8967f938882500bd0ad66f7
Author: almgren <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 35dea3a359e35c1cf52a10be8cac917a69c58ac1
Author: marc <marc>
Date:   Wed Nov 7 00:38:58 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 9479217588812d1db2d7591b7c8e8d0732f14376
Author: lijewski <lijewski>
Date:   Mon Nov 5 23:00:55 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 77990c41aaed91e5e4137f7f00a5ceaf83cc29a7
Author: almgren <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 a2ced314fc1a20aa39375898a214a4253fbe30f2
Author: almgren <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 bccee1710c0479ffbc1b51403eac2b13522caa0e
Author: ajnonaka <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 0e9acd4081828454df1a7e08c4a39485d6df7b60
Author: ajnonaka <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 4c6fd5f6082e71c25f263ad02a605b36774dd522
Author: almgren <almgren>
Date:   Wed Oct 31 20:10:15 2007 +0000

    Fix in set_uu_1d.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit fbe119f4244a2bbddfb8646b2976bb76c4253260
Author: almgren <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 edba9c5fa4824d056095d655d7835a7d82d4032f
Author: almgren <almgren>
Date:   Tue Oct 30 20:50:27 2007 +0000

    Adding 1d routines.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit dc32245e95db0f66bd3067169b22fba68eecb6dd
Author: almgren <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 e14f200078860cbafa98531beb9c17e17372428a
Author: almgren <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 03be5dd822e84f856f952c16fa63f8798a443a94
Author: almgren <almgren>
Date:   Tue Oct 30 20:28:18 2007 +0000

    This version actually compiles.

Src/LinearSolvers/C_CellMG/LO_1D.F

commit e56b47c388e68f5ddb1909732c0d2d4760a2092c
Author: almgren <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 527d1e9e8c01f4b7970e2ed98fa2ea448017f938
Author: almgren <almgren>
Date:   Tue Oct 30 20:10:19 2007 +0000

    Need this in 1d.

Src/C_BoundaryLib/INTERPBNDRYDATA_1D.F

commit b124ea735becde12f15475efee94105ef022f010
Author: almgren <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 c3976590901e0442120601769554a4e59dcd6b19
Author: almgren <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 f1b29261978b395c59537d92f4ab8c80d7c73441
Author: almgren <almgren>
Date:   Tue Oct 30 19:33:52 2007 +0000

    Add 1-d capability.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 0900834bdee8c8272f2e83cce0431c90b4e1e2b1
Author: almgren <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 db54ddb2bc3357b30cd02abcd4358683a0995f8d
Author: almgren <almgren>
Date:   Mon Oct 29 04:03:02 2007 +0000

    Define GetDLogA for 1d as well as 2d.

Src/C_BaseLib/Geometry.cpp

commit 99de2a6741b626d5bfc6d538505b6c3c19dd02cb
Author: almgren <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 1a57649da91a1b6027679773a5058fc7a2db1ff8
Author: almgren <almgren>
Date:   Sun Oct 28 14:46:30 2007 +0000

    Need to include ArrayLim.H, not DIMS.

Src/C_BaseLib/COORDSYS_1D.F

commit b351a4f2aba2d64df8f03a6b52c265bf7c32727f
Author: almgren <almgren>
Date:   Fri Oct 26 04:12:42 2007 +0000

    Change min_width from 1 to 2.

Src/LinearSolvers/F_MG/mg.f90

commit b5b34b458fc61adcae27451873295d6f7917ce82
Author: almgren <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 348b19ca32592af13ddc51e7b10b0bf4e9246915
Author: almgren <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 83f63e502c7561bf786da7e76d5dd7114c71ec66
Author: almgren <almgren>
Date:   Tue Oct 23 17:42:21 2007 +0000

    Fix second call to jacobi_smooth.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit c85d4f87b6bcb960f5d05e63043124930936af3a
Author: lijewski <lijewski>
Date:   Mon Oct 22 20:29:20 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit e3c37d81534f954a9098a5f03f341b3c9b6d89e3
Author: almgren <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 ab3338c0c7d7bc830942ac4c0339a555a056a7a8
Author: almgren <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 22c7ccc25225b40f9579af7f12ae957b268c6a6e
Author: almgren <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 87bf8b8ac707c7924003a9639693427864086f95
Author: almgren <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 508b9beaa618fd45b47a6d7e6d7c389b7421bf98
Author: marc <marc>
Date:   Thu Oct 18 00:00:02 2007 +0000

    fix CVS screwup

Tools/C_mk/Make.mpi
Tools/C_mk/Make.rules

commit 06fead4879a66cac399ed27360a802f2db662eee
Author: marc <marc>
Date:   Wed Oct 17 23:43:53 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi
Tools/C_mk/Make.rules

commit d885427a29e5ee43697f0f13fe408f7cec44f49c
Author: mzingale <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 e24fc09419b818d1813624d36d4f541b05242ef0
Author: almgren <almgren>
Date:   Mon Oct 15 23:07:47 2007 +0000

    Fix calls to stencil_apply...

Src/LinearSolvers/F_MG/stencil.f90

commit c536fe0150f3f39d89e28ece30135a0bd276a698
Author: almgren <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 4e07477aa3a9db2105aaaa9d20bc29f75b830f99
Author: lijewski <lijewski>
Date:   Mon Oct 15 21:11:12 2007 +0000

    added -lrt for FRANKLIN

Tools/C_mk/Make.Linux

commit d8f090440a3c01d4b7b8c6bf04242c7698dc44ac
Author: almgren <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 9798cc658206d269d0909839121bc717183512b9
Author: lijewski <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 befd45a7deb66141eb1623e81ecd9a8a65a723d2
Author: lijewski <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 0902136e6b22b588d2a28bf3fceae93a518dd6e8
Author: ajnonaka <ajnonaka>
Date:   Tue Oct 9 20:22:46 2007 +0000

    Ann's changes in cgsolve.

Src/LinearSolvers/F_MG/itsol.f90

commit c0de87dc6529bab47d6e804b10a502d9c7a079f5
Author: marc <marc>
Date:   Tue Oct 9 00:30:39 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit 055bdc3f4517230bb198c5a7b5dc5789ba432db0
Author: lijewski <lijewski>
Date:   Fri Oct 5 21:52:52 2007 +0000

    more franklin mods for Castro

Tools/C_mk/Make.Linux

commit 5d4579e5e1cccbc0b445b3947aa109bfaaccf593
Author: lijewski <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 1af8f098035d08e224477dfdc5161c4d93fcdfa4
Author: lijewski <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 af01d1325d8032550b3c8e0ac4d3a0651fcf99da
Author: almgren <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 9322cb8eed76bb76a58178046d95009b412e2401
Author: lijewski <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 1586ce83037c7bbb84152505ee64feb04e3059c9
Author: lijewski <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 c5ef13f401b3eb5a455f3bbcd5f169c7320d49c2
Author: lijewski <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 c7d0c6404346a3afdd2aea2286b6bb73fe8b572e
Author: lijewski <lijewski>
Date:   Thu Oct 4 22:31:17 2007 +0000

    added -pedantic to g++

Tools/C_mk/Make.defs

commit 2749a439256500656eb86435f6d53fa74c4c16d4
Author: mzingale <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 18ab2f4db6cab8eb9a5378935019f2103e8f2bef
Author: almgren <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 9110a14c6641c40d211e2532be08ba16c4ef3b87
Author: lijewski <lijewski>
Date:   Tue Sep 25 20:34:13 2007 +0000

    AIX mods

Tools/F_mk/GMakedefs.mak

commit 65a5b4e73f8d350094fd312b95c107e921256796
Author: almgren <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 9f2dca77fd3ea4c31356c8b0f61df8062731dc83
Author: lijewski <lijewski>
Date:   Mon Sep 24 21:29:35 2007 +0000

    added xt4 block for franklin

Tools/F_mk/GMakedefs.mak

commit 809c6b717f698bedc1d3cfeebd87c651e73ac597
Author: lijewski <lijewski>
Date:   Sun Sep 23 18:39:18 2007 +0000

    nan & inf stuff work with PATHSCALE

Src/C_BaseLib/FArrayBox.cpp

commit f012f1bc17d515c7898b6854408e8e93bd58a428
Author: lijewski <lijewski>
Date:   Sun Sep 23 16:44:06 2007 +0000

    inf & nan stuff works on AIX

Src/C_BaseLib/FArrayBox.cpp

commit 47ead16da484dbc0729d6cf16d215b065984ff02
Author: lijewski <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 03fc2bf0383cb51968582482f68ea119373fe762
Author: lijewski <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 86224db16b3c20c44f93099a089de7ce2f0b0231
Author: almgren <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 e8450fed55acd1bc271dcc14db8528ef1726368d
Author: lijewski <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 ad8c69d88af751cd8adab7e16e2288b80613e988
Author: lijewski <lijewski>
Date:   Tue Sep 18 19:57:29 2007 +0000

    floating point format change: es30.20 -> es25.15

Src/F_BaseLib/fabio.f90

commit 991daf6e1371c1f2e84ce94bb23c6fa1868e57d9
Author: almgren <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 dac8519056662baaa08a62046b5dd50cbdf92fe6
Author: lijewski <lijewski>
Date:   Mon Sep 17 21:37:27 2007 +0000

    simplified _nfiles stuff previously added

Src/C_AMRLib/Amr.cpp

commit 6448464f14cafff770489492edf20e8b87c983f9
Author: lijewski <lijewski>
Date:   Mon Sep 17 17:47:52 2007 +0000

    changed defaults for *_nfiles to 64

Src/C_AMRLib/Amr.cpp

commit 009184e0cdccd38e5706a645c5560f1b829ec613
Author: sepp <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 786d7e6528416dbc1563cc4b1d618f2bf77ee9f1
Author: lijewski <lijewski>
Date:   Fri Sep 7 23:01:43 2007 +0000

    can now regrid single-level calculation

Src/C_AMRLib/Amr.cpp

commit ba361e2f63d9424026d8358535614b10ee2391d1
Author: almgren <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 1e25255b3f9ee926e4699660faa477b06685ea62
Author: almgren <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 61d642d1c88e302d991b3bf2d60bff78a4882a12
Author: lijewski <lijewski>
Date:   Thu Sep 6 20:27:16 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit bc6692574107efbdf54a7239565664225283ae89
Author: marc <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 055ebe55e5457570619bdd061a25f68fec774802
Author: marc <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 4fc697882a3578a81d6eb13cd3751dd5c7c1a36c
Author: lijewski <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 a82ffa5953a147e7d7a204fff1aa81260745d022
Author: lijewski <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 d9ccc6310172565a1a41fe41581813d80bc2819b
Author: lijewski <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 83f9ae5c1bb1ee44a37b09f0ec6398de2a32b955
Author: lijewski <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 0ddb88546b289bdabbef0906cdba24905eb79e90
Author: almgren <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 3a5c82e9fb500d4715d0ec6378907a6f3e1429ea
Author: mzingale <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 e1b671f7d7711ef0595a53fd8a575cbd209f5cf5
Author: mzingale <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 9e2ea598fa2aca4636e431fb77ae2ed715621b6b
Author: lijewski <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 40e8fe853a67710d9d97ebfec37c9ed077a02d16
Author: almgren <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 343099aff40261ac0daa360d50697d1159928b7a
Author: mzingale <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 723757c1fe4d5e65843f235d8b02e4c9203755b9
Author: almgren <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 587a3c961c7c27e0491bd00c92f00694d0e6f6ea
Author: almgren <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 e99dc22c282347994a982c6845df924bb7037884
Author: almgren <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 3004e15edc29d01a244b3fe9172d3c9fbbbf47d1
Author: mzingale <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 54ad330a534f637cbea364da453bb2c17f069912
Author: ajnonaka <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 9d3441fb20d978a8c9fb282d761578154c092d45
Author: almgren <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 5e49193b5f9c89056796ddbfd52ae3b487bd554d
Author: mzingale <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 b791b42339476c2cbf7870c821c1f3823d6bda4f
Author: almgren <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 78fbe4dd056443cdfd9bc3881ac906e30df49a28
Author: mzingale <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 2eba167f30172dc54789ccb550f59e5b2028d7aa
Author: mzingale <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 f03c59b90114d99d16dfd85632989cebbf1c89fa
Author: mzingale <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 eec0968fac9057949d2c663675145dbf3b33b98e
Author: mzingale <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 5c3e933d4376e712d0963eaba6bd6c4b2be941f9
Author: mzingale <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 dd114a9aaf49c99537077edb31a0fbdd9295b0ee
Author: almgren <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 bfdfb64deb561270e05914cab8a22dca8055184b
Author: almgren <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 c3e6c7cbeaf29cc8d2cd9e78d9e7dd4490bb23b0
Author: almgren <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 c1987f970807c4eb5ff82c73383e46b278520aa7
Author: almgren <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 145e5e7e9db211df660f0b65f8bc5eed0731e122
Author: mzingale <mzingale>
Date:   Wed Jul 25 20:34:31 2007 +0000

    make the string length a script parameter

Tools/F_scripts/make_build_info

commit c5720ea4e3785ad55b6e5f086b06e4a3145ead4f
Author: marc <marc>
Date:   Wed Jul 25 01:07:35 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.CYGWIN_NT

commit c89b062764143930c093290aff7c750bf037e8e9
Author: almgren <almgren>
Date:   Thu Jul 19 21:04:33 2007 +0000

    Added function ml_resid.

Src/LinearSolvers/F_MG/ml_cc.f90

commit 283e233c4ca2bd9e5ca55fa3a5bdf420654bb6a2
Author: mzingale <mzingale>
Date:   Thu Jul 19 18:49:58 2007 +0000

    add some more comments and documentation

Tools/C_util/Convergence/DiffSameGrid2.cpp

commit 9df4df2dd4fbcda8f308c7abc8374bb3abb5ea89
Author: ajnonaka <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 82a8028889ce05d0c2d9c04c20a1ee7a4a1cb690
Author: ajnonaka <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 0fbd29afc747c05c55791c17ceae1ed11e0ccb0d
Author: ajnonaka <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 c03bdff8c047c400055cb3314c7001d3e394c8ec
Author: mzingale <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 8ad52aa75b8fcf308d3d17f1014ec82d63869888
Author: mzingale <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 ca5b6a89df38988d49295de2f5c0f91b82e1091e
Author: ajnonaka <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 3aeb58aa62577b8d3e09aee2a6ee6fbbf979f5ef
Author: almgren <almgren>
Date:   Tue Jul 17 05:15:37 2007 +0000

    Fix small typos.

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit ff1b5693c7377b4c5b57aca4763bfe4f1725ceb6
Author: almgren <almgren>
Date:   Tue Jul 17 05:06:33 2007 +0000

    Needed 3d instead of 2d...

Src/LinearSolvers/F_MG/mg_cpp_f.h

commit 76fe970bf5143d05c4ce42a953595be21f1fa671
Author: almgren <almgren>
Date:   Tue Jul 17 04:46:18 2007 +0000

    Remove print statement.

Src/LinearSolvers/F_MG/stencil.f90

commit 7ca08308b319b85186284e51296fee6d8b171f88
Author: almgren <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 49ef3a5a2419a8e26f2f5fa8cf81ba2c981b5733
Author: almgren <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 6e7c7f7747aff070a77421560c61ce75edbc124c
Author: almgren <almgren>
Date:   Tue Jul 17 04:15:31 2007 +0000

    Change name for timing routine.

Src/LinearSolvers/F_MG/mg.f90

commit 46ceee345196130fcb10969c3135dab5960ceba3
Author: almgren <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 dd792243c383c13ef9838534bcafdf6a9410c8fb
Author: almgren <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 014054a7f71a73e136456a7a02c44a34ec700c0f
Author: mzingale <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 29eb1cb45934ceb580b863ca023b87d924a52f30
Author: almgren <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 4de2a124e9d45a4e270ec72365f3e33dc5c4661e
Author: almgren <almgren>
Date:   Sat Jul 14 00:35:45 2007 +0000

    Remove extra print statements.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 80244be905d918471cc8b7a49f809d3c7ffe0c7e
Author: almgren <almgren>
Date:   Sat Jul 14 00:16:46 2007 +0000

    Remove print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit cc05121eb62801ee55c803ca6db59757061656fe
Author: almgren <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 8eadcecc8082623170481464b8d5cabe62076d83
Author: almgren <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 f20ff73120d3a87bd22815928110f0211599b4d6
Author: mzingale <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 043ed38d0229483082982a0c33beadffa6f828ed
Author: mzingale <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 8b42615f5bd17c833584560956cc9a3e3438a9b7
Author: almgren <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 5eacacf3e92dcfbd2152b35d5b0f7d6793020ffc
Author: ajnonaka <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 3546b63aca105b385312b661a1cf5a187d40da01
Author: almgren <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 a07c1a10a0263248bf388a07f3381b1c12f8ac63
Author: lijewski <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 55201d704c732512c3b1f260828306addb349f4a
Author: almgren <almgren>
Date:   Thu Jul 5 20:51:20 2007 +0000

    Get rid of unused gbox in assertions.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit d3f1290b7f42162e3f2b5ea942efde60b07e0457
Author: almgren <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 1f143e98d4827a70544070d827e544c87126e3b7
Author: almgren <almgren>
Date:   Thu Jul 5 20:49:18 2007 +0000

    Fix up the MyProc stuff.

Src/C_BoundaryLib/FabSet.cpp

commit 3b24bf6b6f9bbda70db6881b1954e0472d1faa8f
Author: lijewski <lijewski>
Date:   Thu Jul 5 20:43:08 2007 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/StationData.cpp

commit 4f3198393055a9cfa83e612fec32e219cb494fdc
Author: lijewski <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 6e9eca51bf4623f7c7b4d75684122c234f42cca1
Author: lijewski <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 8e0135b01e104b1a807ad9ce8ae4d33d51a5f9af
Author: lijewski <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 48dc62e9ac5952bd7ed609909ab48bb072fe07c3
Author: lijewski <lijewski>
Date:   Tue Jul 3 21:22:57 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 83dd3209220924f53f20bb6bd854dddb36c5a88b
Author: almgren <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 1d0cd47cee590ae52ed9d66b125baf1843b2b9f9
Author: almgren <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 ab9125ff53fabd9ec3001988f1ab98ebe3193574
Author: lijewski <lijewski>
Date:   Tue Jul 3 20:10:56 2007 +0000

    g95 stuff

Tools/C_mk/Make.defs

commit 95e1a6a6e4f65522f6b640ef0e9da838a1cdf4f0
Author: lijewski <lijewski>
Date:   Tue Jul 3 19:50:33 2007 +0000

    removed extraneous OutOfMemory

Src/C_BaseLib/BoxLib.cpp

commit dc084c10230144693998c3956cad4a0bf1783c79
Author: lijewski <lijewski>
Date:   Tue Jul 3 03:37:57 2007 +0000

    removed stencil_flux_fill_st()

Src/LinearSolvers/F_MG/stencil.f90

commit 1ee15658dd37fd31a751de4795a56d67e2a61e58
Author: lijewski <lijewski>
Date:   Tue Jul 3 03:13:09 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit e8221def5fed47c26b3ea7f0df9770585750262c
Author: lijewski <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 68824b03f8853d869bdb977ada9329051dd8f8d4
Author: lijewski <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 89b95736137485ff704b81898beec60dfffadf37
Author: almgren <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 4d336d4c5ecf8959894d812d53b6fe0440bc578d
Author: almgren <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 5857a4cd2867c2532a236ccf92ffb3c5efcb82d9
Author: almgren <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 88dc7c1c24e7dd7fb996dbd2b3c8bf64c9f9f425
Author: almgren <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 c9cc54d569bbf8d97fe3d6545556596b40c78a20
Author: almgren <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 4e54a883d614f342b617b3187ca815f36a6f7cb1
Author: almgren <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 6c9fcb8005d56cb045a648cbc68ac0c5e9ac9498
Author: almgren <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 ebba28515abb61695c8ef743ad840e25f5410b66
Author: mzingale <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 ba5906adcb53e87c2043551b3445c4725d8ddc06
Author: sepp <sepp>
Date:   Fri Jun 29 17:06:45 2007 +0000

    1) more adjustment of spaces in comments

Src/C_AMRLib/BC_TYPES.H

commit dd611f01c79fad385b60c7236ea7237448fefedf
Author: sepp <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 ea0cd0ac16913dd306353d7f1dcc86ef5ecfb04f
Author: almgren <almgren>
Date:   Thu Jun 28 20:29:56 2007 +0000

    Removed another print statement.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 309c90827cd6ae88134bf79bf7b33d92686bf2c4
Author: almgren <almgren>
Date:   Thu Jun 28 19:41:20 2007 +0000

    Removed write statement.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 469518e3b1331b5bd42f4182f605fe160a825fd1
Author: almgren <almgren>
Date:   Thu Jun 28 19:41:07 2007 +0000

    Removed print statement.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 5bcd584817c7a1eb740851c81b8a6d528fc78e3b
Author: almgren <almgren>
Date:   Thu Jun 28 18:46:59 2007 +0000

    Get rid of print statements.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit b0892ba83137aeab0216169459d81483f8847d46
Author: almgren <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 4de8d0a58b2041ee681ab70e18493433f93c2eb6
Author: almgren <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 11b54e139f65b50c196674a2a71490a654b88ad2
Author: almgren <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 f76bc9ae57b61052c8921f6aae10e237f04562ab
Author: almgren <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 4b4be06d9ed5771a3ed985a56c60a11b2ffe6399
Author: almgren <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 23ce8e919e3bd3b6358fe6dfee31cac2894535ef
Author: lijewski <lijewski>
Date:   Mon Jun 25 22:54:26 2007 +0000

    only run f90.depends on f90EXE_sources

Tools/C_mk/Make.rules

commit bd4af21641ed60fd1a6016b09d7993752f9c3a61
Author: mzingale <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 3b56faaf788650746bae93789c4d6f211b13d60d
Author: mzingale <mzingale>
Date:   Tue Jun 12 12:20:21 2007 +0000

    add Intel 10.0 compiler support

Tools/C_mk/Make.defs

commit da394d5f116b6cfa1c11394fa714dc8d35e0dedb
Author: almgren <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 4966cc88cffb4c52ff8f2822eec9a92564ee5c45
Author: almgren <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 452a67ccfe4c0d3895ee796ba9aabd6d7a35c880
Author: almgren <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 5071974b7d63ba389267010cb74a9562290aa19a
Author: lijewski <lijewski>
Date:   Wed May 9 19:52:05 2007 +0000

    Added reduce_real_sum accessible from Fortran.

Src/C_BaseLib/ParallelDescriptor.cpp

commit f4934c313fced2520b794c69d6d49e7a356e3504
Author: lijewski <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 783acf80a83a35487b7dad0dfc237cac2b503d01
Author: lijewski <lijewski>
Date:   Wed May 9 17:55:29 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 449bf8c4f5c3cede01d25406ed22b2da4b8365c9
Author: lijewski <lijewski>
Date:   Tue May 8 21:01:15 2007 +0000

    faster sort() in simplify()

Src/C_BaseLib/BoxList.cpp

commit 92c1996b2b8b0252563bdbb5d5354f8fc2a939a0
Author: lijewski <lijewski>
Date:   Tue May 8 20:08:21 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 084ffa6cc8b8c9093c889d9d7c14f002622f159f
Author: lijewski <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 31be6c2c25b9753116be385c8a58e88605a6e8c8
Author: lijewski <lijewski>
Date:   Tue May 8 19:26:35 2007 +0000

    now simplify() in batches of 50 not 250

Src/C_BaseLib/BoxList.cpp

commit b6d9d835835716e2e1a3c22e40f08d67826834e7
Author: lijewski <lijewski>
Date:   Tue May 8 19:02:45 2007 +0000

    assert ngrow>=0

Src/C_BaseLib/FabArray.H

commit 82586616075cf95b1cf73c7537c22b6bdb310ed4
Author: jbb <jbb>
Date:   Tue May 8 16:35:31 2007 +0000

    change

Src/C_AMRLib/Amr.H
Src/C_AMRLib/Amr.cpp

commit 17f34706fafc53a9106eb8089d3aaafcc5f4889d
Author: lijewski <lijewski>
Date:   Tue May 8 03:30:43 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit c9a080fed69b8ec7fc95d85cd893b68743fe02c7
Author: lijewski <lijewski>
Date:   Sat May 5 20:54:12 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit d2cc24e0b46fe729d5f2bb0de2d2323253710c21
Author: lijewski <lijewski>
Date:   Fri May 4 23:21:24 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit 2152c0b8e454343555b1fa254d13a82b92a4c1b9
Author: lijewski <lijewski>
Date:   Fri May 4 23:00:51 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Cluster.cpp
Src/C_BaseLib/BoxArray.cpp

commit 8455340dc3e4c5e2a1d7cceec18d3d9ff4ba9526
Author: almgren <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 fba93fa3c5efc4493d92719291ca732d8c1465e8
Author: almgren <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 5c0c75d9a60cd676335516a77ef6738da5c3e065
Author: lijewski <lijewski>
Date:   Fri May 4 19:08:48 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxList.cpp

commit 5e7834214c96b7e24b79cb472eca7c95c0b0f594
Author: lijewski <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 861db38e4f24c6c8558fdf848ff5c7f0bc586668
Author: lijewski <lijewski>
Date:   Wed May 2 21:53:15 2007 +0000

    added FastContins()

Src/C_AMRLib/Cluster.cpp

commit e178ee01979a36cd758c39e1c88e74e5fece4910
Author: lijewski <lijewski>
Date:   Wed May 2 21:49:24 2007 +0000

    shortcut for special case of complementIn()

Src/C_BaseLib/BoxList.cpp

commit addcbf0f361315846f9fdbd6ff015846c3b4a1e0
Author: lijewski <lijewski>
Date:   Wed May 2 21:48:19 2007 +0000

    more profiling

Src/C_BaseLib/BoxArray.cpp
Src/C_BaseLib/BoxDomain.cpp

commit de855822d45e32914aa817b17e3fca2750e91596
Author: lijewski <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 741ed35a5b8dd6f0abe7a8d3591e152ff4cdeca0
Author: lijewski <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 421b2312709b9f1d5cde9144082fbcc6507be375
Author: lijewski <lijewski>
Date:   Tue May 1 22:42:34 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit 60e2d138ff17ba9839283fe30936458df8f9ad57
Author: lijewski <lijewski>
Date:   Tue May 1 22:26:03 2007 +0000

    comment out simplify in grid_places() for now

Src/C_AMRLib/Amr.cpp

commit a78b8bddb5559600dbe77594d95ab6c075730795
Author: lijewski <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 1e5eaf26fcc1276598589ccc0757f5dd747f19f1
Author: lijewski <lijewski>
Date:   Tue May 1 20:11:02 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit acb00607d0fcda635bd41ea9f7120227fcfd7c8a
Author: lijewski <lijewski>
Date:   Tue May 1 03:12:50 2007 +0000

    ProjPeriodic() now does a simplify()

Src/C_AMRLib/Amr.cpp

commit 83aa2764ec2f5403f31237d239be495ed9fe2152
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:57 2007 +0000

    Initialize() now does full simplify()

Src/C_AMRLib/AuxBoundaryData.cpp

commit f29560f565ee0bb16c7d9dc569edf463f76d7d2a
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:32 2007 +0000

    complementIn() now does full simplify()

Src/C_BaseLib/BoxList.cpp

commit 4fe7164d4d413c5bf7d4611f604ba5fdfe8ed51b
Author: lijewski <lijewski>
Date:   Tue May 1 02:59:20 2007 +0000

    removeOverlap() now does full simplify()

Src/C_BaseLib/BoxArray.cpp

commit b8fed644ff5bc924c72130414fd96e4577728372
Author: lijewski <lijewski>
Date:   Mon Apr 30 21:07:14 2007 +0000

    a really big HCAll grid

Src/C_BaseLib/test/ba.95860
Tests/C_BaseLib/ba.95860

commit e8daaf99f1363b60e47f8262c8195682fe2cf9ec
Author: lijewski <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 3e4157c4910a7e781a7729e423b98a62b8dbcc77
Author: lijewski <lijewski>
Date:   Mon Apr 30 20:54:58 2007 +0000

    sped up simplify()

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/BoxList.cpp

commit 3b6fc52796bd6663f684e85c5a16b1d785030186
Author: lijewski <lijewski>
Date:   Wed Apr 25 20:02:34 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 7bf9c341375658a68e894cced36db92f4126e6bb
Author: almgren <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 43234e5ca1bf3b4b12b54af0abfbe76d414af67b
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:13:08 2007 +0000

    *** empty log message ***

Src/C_BaseLib/test/ba.15456
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
Tests/C_BaseLib/ba.3865
Tests/C_BaseLib/ba.mac.294
Tests/C_BaseLib/tBA.cpp
Tests/C_BaseLib/tDM.cpp

commit 32c188923337b771b2852877719df40da8bfb5d5
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:12:42 2007 +0000

    improved SFC; sfc_threshold now 10

Src/C_BaseLib/DistributionMapping.cpp

commit 0dd0c8c16f28298dcd345b06adfbab7b1ef9d356
Author: lijewski <lijewski>
Date:   Tue Apr 24 21:05:46 2007 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/ba.23925
Src/C_BaseLib/test/tDM.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/ba.23925
Tests/C_BaseLib/tDM.cpp

commit a17d3683edc0d513106f9804f81d40add84aa5ca
Author: lijewski <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 f62c7dcfbb5a8348b3f43bab972a07d32dfa8bc2
Author: almgren <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 ccd278d17a7ceb4774cb0dbff1d2be8248861344
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:50 2007 +0000

    commented out simplify() in grid_places()

Src/C_AMRLib/Amr.cpp

commit 4c143ac7a809b2263fb379f4403daa83d62e8d30
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:20 2007 +0000

    commented out complementIn() in removeOverlap()

Src/C_BaseLib/BoxList.cpp

commit d7a2f6db4a65332e83d1eed6347202caea08b47c
Author: lijewski <lijewski>
Date:   Tue Apr 24 01:13:06 2007 +0000

    commented out simplify() in removeOverlap()

Src/C_BaseLib/BoxArray.cpp

commit 83dc414139a409859d12447678e64e3863c60093
Author: nazgul <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<MultiFab>.  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 e1e6336a9fc339f7af2129ae89a4e7b8d95ae993
Author: nazgul <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 8b1c8c74b4452e9775ddc889804a59b2dc987dc8
Author: lijewski <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 7e925e972683a274d17673466011fd616d258baa
Author: lijewski <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 f9a784d6ac733e978bef05bbd082452d2d9d4423
Author: lijewski <lijewski>
Date:   Fri Apr 20 21:26:56 2007 +0000

    default for sfc_threshold is now 10

Src/C_BaseLib/DistributionMapping.cpp

commit 914c5412d74865bbab1e741f0ca40c1582ec31fa
Author: lijewski <lijewski>
Date:   Fri Apr 20 20:55:44 2007 +0000

    verbose now defaults to true

Src/C_BaseLib/DistributionMapping.cpp

commit 103da9ee73c80dc9c406633f152ab2343c984712
Author: lijewski <lijewski>
Date:   Fri Apr 20 19:13:58 2007 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 94de005abcbc104e3bf8f2392c78610add28f8a7
Author: lijewski <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 783f46821775fb46d2f9e92a3442d49edcd76c88
Author: lijewski <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 1ad917d5be758fed4499be1bdebc2a3d5261e7d5
Author: vince <vince>
Date:   Thu Apr 19 01:23:22 2007 +0000

    added a knob for calling probinit.

Src/C_AMRLib/Amr.cpp

commit 6ec5f322b6d7d04977a610417167be94f1a78cac
Author: vince <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 cdff5c62de34cfdf069c9762f3841e46a69adf56
Author: vince <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 d2585bb33f6ea6385dede18c3410b576629393f3
Author: vince <vince>
Date:   Thu Apr 19 00:17:49 2007 +0000

    added code to limit probin opens.

Src/C_AMRLib/Amr.cpp

commit 6e1f042345e8316d5bcb484e01fd534a6618f992
Author: lijewski <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 26565df2e2cebe1e2c499cfa369ad3c09bfc29e7
Author: lijewski <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 29706d1a803d3de38b9227d6ef04e9c0d1674ffe
Author: lijewski <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 e72baa65d5df91303ae3bbf04791548683e55c46
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:28:03 2007 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 155a0e88006db106b72a28fefd4b664ad70ce059
Author: lijewski <lijewski>
Date:   Wed Apr 18 17:27:28 2007 +0000

    added -Wno-deprecated for g++

Tools/C_mk/Make.defs

commit 34bdea67fe23c8862df5e5bb7ff6cfde85fa4f60
Author: lijewski <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 1af6469ca5f3b7e1f2b4850992873e92ef46721a
Author: lijewski <lijewski>
Date:   Tue Apr 17 18:12:14 2007 +0000

    added AuxBoundaryData

Src/C_AMRLib/Make.package

commit deaca49594e733fc454b26f843f2c8be8e3c5ec8
Author: lijewski <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 9a6cb64cda7cb9865ff9b3c1d75a9a324c3265cc
Author: lijewski <lijewski>
Date:   Tue Apr 10 20:16:27 2007 +0000

    needed <string>

Src/C_BaseLib/ParallelDescriptor.H

commit 8c255ccffdc0d70888404b2038573432cabb516d
Author: lijewski <lijewski>
Date:   Mon Apr 9 20:29:45 2007 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 2746b0ee389686501d94cff17692227a60b0c7ad
Author: vince <vince>
Date:   Fri Apr 6 22:31:42 2007 +0000

    another friendly read.

Src/C_BaseLib/ParmParse.cpp

commit 7eb5ef4292ac8c8131da7a51a88bef355fbaa98a
Author: vince <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 c737e279be241242160246b1f453bf01b26c9c56
Author: lijewski <lijewski>
Date:   Wed Apr 4 05:14:10 2007 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit bce34c7fa6833d459222710b29de22e550e1b8dd
Author: lijewski <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 b63e80657a15438dd89c0a09caa1802f2da03f89
Author: lijewski <lijewski>
Date:   Tue Apr 3 23:34:55 2007 +0000

    add ability to turn off LeastUsedCPUs()

Src/C_BaseLib/DistributionMapping.cpp

commit f7b1d7f191daa4eeb12534f62bbc80b35c0bae81
Author: lijewski <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 db0aa774caaef638ac6d62e4c1a13a5cf513c550
Author: lijewski <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 6aeadc1b5577d37d16be67f1577ed631b3ea9b94
Author: lijewski <lijewski>
Date:   Thu Mar 29 18:12:44 2007 +0000

    removed T3E stuff

Src/C_BaseLib/FPC.cpp
Src/C_BaseLib/Utility.cpp

commit 614aa7b56f8c8dffd1acf257e1f855ae353477bc
Author: lijewski <lijewski>
Date:   Thu Mar 29 18:08:50 2007 +0000

    XT3 stuff

Src/C_BaseLib/Utility.cpp

commit 4bdc2c36e71303c0303ff6e4593ad0dda4baeb1d
Author: lijewski <lijewski>
Date:   Thu Mar 29 17:57:25 2007 +0000

    XT3 stuff

Src/C_BaseLib/Utility.cpp

commit e15e9970fda6edea417d398b83f0d5ffbe66dd6c
Author: lijewski <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 c2100b0f8c7209b26c6a2b8d5efe80d084f5bea9
Author: lijewski <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 f760a8a1eeee4e07ba64ace526c08d5eec1851be
Author: lijewski <lijewski>
Date:   Thu Mar 22 16:24:40 2007 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit 9b91aa0bf31515769ce46fb98272f87948c25312
Author: lijewski <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 1b13c4c02ad1f99176c6ea82b6051b9c83248807
Author: almgren <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 74763270b81554e61f6f04d464fa6fbeed1823f2
Author: lijewski <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 240d35f35fd3f9752f9a9e52171dabf53fd6c703
Author: lijewski <lijewski>
Date:   Tue Mar 13 21:35:54 2007 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit ff04a5c947efab92e3c15de02e707c0db1d86365
Author: lijewski <lijewski>
Date:   Tue Mar 13 17:01:23 2007 +0000

    SFC is now the default

Src/C_BaseLib/DistributionMapping.cpp

commit 2722b88f65696221163badfb9978e31c45cef799
Author: lijewski <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 405a72db47994157a98e34f5bb8bd1096c5450ec
Author: lijewski <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 e39f0a146bb3c4d9c99c8c98b5569e7d381c95f4
Author: lijewski <lijewski>
Date:   Thu Mar 8 22:19:39 2007 +0000

    XT4/PGI

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 8742b75bf35f120d3fbefe00d0f8b9a51a986942
Author: jbb <jbb>
Date:   Wed Mar 7 18:21:02 2007 +0000

    atlas changes

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 4d241532039da45e0daf1d8dc3801e948e8e3501
Author: lijewski <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 b6657bca34893101ae82f3fc3afe5cc0bd9d3fbf
Author: lijewski <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 a74137bb60c93dd5cc34dd9692383d9fd4a26808
Author: lijewski <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 cf7d48c11f5a683952bedf8b86df6e1af1b3c3ca
Author: lijewski <lijewski>
Date:   Sat Feb 24 00:04:59 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.15456
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
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 b454fd3afa7bafd2b474b2b6d0eba10f51f2ee6e
Author: lijewski <lijewski>
Date:   Fri Feb 23 23:05:57 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 6a8a7109e2b5eb7b60b8b0fd95957736a9057038
Author: lijewski <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 e02311abc7ce92ae727e1f9b9a67586c3856f02b
Author: lijewski <lijewski>
Date:   Fri Feb 23 21:42:23 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.15456
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
Tests/LinearSolvers/C_CellMG/grids/in.grids.15456
Tests/LinearSolvers/C_CellMG/grids/in.grids.5034

commit 2394aaca73d47fc5bc88992672d0c5eebf601304
Author: mzingale <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 e6d5e04a895ba85fdd16d467e8064fdff7ab20d2
Author: lijewski <lijewski>
Date:   Wed Feb 21 21:36:51 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/Test/grids/grids.25600
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
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 37f394524eb0765f0dc20047aba0af1af64c431c
Author: mzingale <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 a6570ee5d84bc59f6262d2b40b8885373b6da663
Author: mzingale <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 6b51163cdc9dc951dea6895bbf2d2fff5c868634
Author: lijewski <lijewski>
Date:   Wed Feb 21 17:19:34 2007 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit cf8f201f0b3028909d5cc72413d9e5b78263e661
Author: lijewski <lijewski>
Date:   Tue Feb 20 18:30:33 2007 +0000

    print out grid distirbution with boxes

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 2f899f71fa818959ff545ce132e79e56bd836f00
Author: lijewski <lijewski>
Date:   Fri Feb 16 21:18:22 2007 +0000

    set eps_rel to 1e12

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 527bd14f4104df279d68ab3ec0ab8bebf2e7b202
Author: lijewski <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 7438688d246e65db63d4809f119a7b6f3b85108a
Author: lijewski <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 d855590437cc587927bf49b53b1e47209b1b1955
Author: lijewski <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 aff4aa5096152f718dc56050d6598015ef5fe91d
Author: lijewski <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 e5f1683f63605ec62c04e30c1f7e615ecf810ae7
Author: lijewski <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 a5f038c21ea7a79b9c8b34ada2e4cc176eb119f8
Author: lijewski <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 d2e4d44a32c0c50f4dcf04c716e1bcc149ecb3ba
Author: lijewski <lijewski>
Date:   Fri Feb 16 00:02:37 2007 +0000

    use hash method for calculating masks

Src/C_BoundaryLib/BndryData.cpp

commit 0e37c9b07f51028a31f78c162386c72d3ed0aeec
Author: almgren <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 29f311fe59b488b8a620cecafa83ca53a62876da
Author: lijewski <lijewski>
Date:   Fri Jan 26 20:16:45 2007 +0000

    ParmParse'd fpb_cache_max_size

Src/C_BaseLib/Geometry.cpp

commit e815a67b82dffdb6b5bfbc58b971b3fddd965efa
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:23:40 2007 +0000

    *** empty log message ***

Src/C_BaseLib/MultiFab.cpp

commit f35ee336f07db3b809525c60558375924636c75b
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:17:09 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BaseLib/MultiFab.cpp

commit a43cba76c40b705ebaef8923cf0126ec3de082e7
Author: lijewski <lijewski>
Date:   Fri Jan 26 19:03:14 2007 +0000

    *** empty log message ***

Src/C_BoundaryLib/FabSet.cpp

commit 4bce76e693c18b43a56d0aa5a065d40b2a2e70f9
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:47:45 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BoundaryLib/FabSet.cpp

commit 1e4f0e366c7f94e34022207b0da57ab812c2fe00
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:26:04 2007 +0000

    ParmParse'd copy_cache_max_size

Src/C_BaseLib/FabArray.cpp

commit 1734bde3900c772a27c31b483afad528b052aa08
Author: lijewski <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 f6ecab07a285c8a606a18432d9352332fd750968
Author: lijewski <lijewski>
Date:   Thu Jan 18 17:22:19 2007 +0000

    extra assertion in define()

Src/C_BaseLib/FabArray.H

commit 775a826538e3797348612edf4ece8b4aa0dc6d9c
Author: lijewski <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 cacb232aec2592fa496a4f0a3456436960f63a03
Author: almgren <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 efb08bbbeaf0ebe6b0eddbfd7856498bb4026c6d
Author: lijewski <lijewski>
Date:   Thu Jan 4 20:43:26 2007 +0000

    oops

Src/C_AMRLib/FluxRegister.cpp

commit 7aeb75a42883ee29bad9135b9241e88eae505fa1
Author: lijewski <lijewski>
Date:   Thu Jan 4 20:41:18 2007 +0000

    fixed bug hitting coalescing memory manager

Src/C_AMRLib/FluxRegister.cpp

commit 03ce90eb45bc33aea9accb319a6aaeeed0f2ec61
Author: almgren <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 a96dd0de47e936aa03496bcb9ca46516332cf0ad
Author: lijewski <lijewski>
Date:   Fri Dec 8 20:40:29 2006 +0000

    changed some verbose stuff

Src/C_BaseLib/DistributionMapping.cpp

commit f5b960794ffee797a4723f9cd03fd1ec2109559e
Author: almgren <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 33f71937ecdc839ccff5ca7760000270f9661ca0
Author: almgren <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 8ce0c6582e1fc8803904189496a37ceb446a3ccd
Author: mzingale <mzingale>
Date:   Fri Dec 1 15:45:33 2006 +0000

    some gfortran fixes

Tools/F_mk/GMakedefs.mak

commit 3e824591b3a86ac2afe56344f49559ba8c03b47e
Author: lijewski <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 c3bebdd6a2beba4d119acf61212d12f6c65e968c
Author: lijewski <lijewski>
Date:   Tue Nov 21 23:38:57 2006 +0000

    changed sfc_threshold: 4 ==> 8

Src/C_BaseLib/DistributionMapping.cpp

commit ac29bbc595772ce78c802c654b5ccf1d3f2d2897
Author: lijewski <lijewski>
Date:   Tue Nov 21 06:25:50 2006 +0000

    more SFC tweaks

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 5a065a55a49e0addd3479c02de20a206d589a0ff
Author: lijewski <lijewski>
Date:   Sun Nov 19 04:09:13 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 361fea84c0fd2cf5bb608e29ba05feb1a713a360
Author: lijewski <lijewski>
Date:   Sat Nov 18 05:07:25 2006 +0000

    removed embedded CVS ID

Src/C_BaseLib/DistributionMapping.H

commit 7a7bbb18e9237aaadfbe3dbc1b7f3aab6fe51de7
Author: lijewski <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 5c7d27314f831c90b9a5495031f7c5804127c896
Author: almgren <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 7743810d8dff738690a5fa4167042eaa8914e4b0
Author: marc <marc>
Date:   Thu Oct 12 16:45:12 2006 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 2b32ab247e7a3161cf264df582bc7c9fee1308d2
Author: lijewski <lijewski>
Date:   Wed Oct 11 18:15:08 2006 +0000

    added defined()

Src/C_BaseLib/FabArray.H

commit 9b807943fb99b02c50815ea9142422dd71c883e3
Author: sepp <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 e5a0578d4b34d08dd0582aa09dd985ace6881471
Author: sepp <sepp>
Date:   Fri Oct 6 17:06:30 2006 +0000

    1) correct syntax in comment block

Src/C_BaseLib/ParmParse.H

commit 5b57af7f2e1e7a05a2f258de7a9a07162eb18584
Author: lijewski <lijewski>
Date:   Wed Oct 4 22:27:04 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 69ccf2d188d2f64e20915931ca08b2d6c4608e85
Author: lijewski <lijewski>
Date:   Sun Sep 24 00:40:19 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit fbb75c95498eba237995ccd7d107eaa5b89251f9
Author: lijewski <lijewski>
Date:   Sun Sep 24 00:32:57 2006 +0000

    now print out top 5 communicators

Src/C_BaseLib/DistributionMapping.cpp

commit 3797ca98f4e13b6fb872e276fe502e6222a2cea6
Author: almgren <almgren>
Date:   Sat Sep 16 03:20:59 2006 +0000

    Fixed extra endif.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 6db4a5ec58478b28fde9e6084116e824b576c5be
Author: almgren <almgren>
Date:   Sat Sep 16 00:52:54 2006 +0000

    Fix weighting of different stencils.

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 25d5f0ec8fa549e5e23570967a022276cd7af50c
Author: almgren <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 addb5daabdb98ba79f96b763ada39ad4dc4989a3
Author: almgren <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 8a5a1584811325f916f99f197eb0da8df5bfda05
Author: almgren <almgren>
Date:   Sat Sep 16 00:51:35 2006 +0000

    Small cleanup.

Src/LinearSolvers/F_MG/nodal_divu.f90

commit d96ae34547005e07053994ab21bf668ffba6ce61
Author: almgren <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 02af82104b06271d78e3ab115dbad0b385e001cb
Author: almgren <almgren>
Date:   Fri Sep 15 23:57:51 2006 +0000

    Fix print statement.

Src/LinearSolvers/F_MG/mg.f90

commit 0de7e31b9c907e22cda8ae369b4a588243764490
Author: almgren <almgren>
Date:   Thu Sep 14 21:03:49 2006 +0000

    Remove "NXC" print statement.

Src/F_BaseLib/interp.f90

commit 02ae4bdbe7ef0debb69472796dc2c04243cc25b3
Author: lijewski <lijewski>
Date:   Thu Sep 14 19:57:27 2006 +0000

    *** empty log message ***

Tools/C_util/Convergence/GNUmakefile

commit 6f605244afcce7a89286f40ecb795b6a9685c3e9
Author: lijewski <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 ed200285f17ce81f87d32ecd953201575f8029e6
Author: lijewski <lijewski>
Date:   Wed Sep 13 20:28:00 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit e3128968528cee436cc1144c3dec464520059094
Author: lijewski <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 a59a02cba92fdbe0cd45b56b29098fa1de8d06f1
Author: lijewski <lijewski>
Date:   Tue Sep 12 22:51:04 2006 +0000

    refinement to FPB caching

Src/C_BaseLib/Geometry.cpp

commit 9a34a49dee49973658cfe610e34d76d3e01ab826
Author: lijewski <lijewski>
Date:   Tue Sep 12 21:50:09 2006 +0000

    refinements to caching

Src/C_BoundaryLib/FabSet.cpp

commit 393c70d5c1b319b660f68ae80840b8636e0f5484
Author: lijewski <lijewski>
Date:   Tue Sep 12 21:38:45 2006 +0000

    *** empty log message ***

Src/C_BaseLib/MultiFab.cpp

commit 4378d712289e9d0c7abd5d27c40204d843d6067b
Author: lijewski <lijewski>
Date:   Tue Sep 12 20:46:46 2006 +0000

    refinement to FillBoundary caching

Src/C_BaseLib/MultiFab.cpp

commit 4a41e4035435623d65a2f282599de27e3652a84c
Author: lijewski <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 d053719564df013263ffe76b1b00604501ff201f
Author: lijewski <lijewski>
Date:   Mon Sep 11 21:43:39 2006 +0000

    flush copy() cache on regrid

Src/C_AMRLib/Amr.cpp

commit f417de25ca058949715ebfc93fe63f259ab1c679
Author: lijewski <lijewski>
Date:   Mon Sep 11 21:43:20 2006 +0000

    added copy() caching

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/FabArray.cpp

commit e30769dad88a75c430c2415394a1f5fdddfa3e16
Author: vince <vince>
Date:   Fri Sep 8 23:17:20 2006 +0000

    change for jvn.

Src/C_BaseLib/VisMF.cpp

commit 112143b8f019ad0d23677ac1b299c8a0ee9a1f17
Author: vince <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 f9146825ff22b0da3b47624df71dba132b1671e6
Author: almgren <almgren>
Date:   Thu Sep 7 18:30:22 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/GPackage.mak

commit c8f63ceb12775c2155b6515ce50e8d8f20805d81
Author: lijewski <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 91ed7ebe277faaf69089e4f19cf465a8e95b0f02
Author: lijewski <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 33959afafc331447dadf20acf7ffb2384c888e52
Author: lijewski <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 552cb18f27869a34aecd14653d6b5126f24a547d
Author: lijewski <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 d8d1d806806b8ed56dd1fa6623de78a84cca82c3
Author: almgren <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 5ecfc8cf81b78b2178b4357931376786103359e1
Author: almgren <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 a157b0c1bb835dbffef83d042ffaba1b385ce9c1
Author: almgren <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 75ec3b29c6d38008c6fefd7ce1eb5662a6f7c2ce
Author: lijewski <lijewski>
Date:   Fri Sep 1 16:24:17 2006 +0000

    removed METIS stuff

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 63399f7fc0cdadaf3729ce182309bd88064c5162
Author: mzingale <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 48eae2f061e707cf5ed5119b84ff213684075bb0
Author: mzingale <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 3fedc02adfdb891635f14d69b63558a6ab74bafa
Author: lijewski <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 85c990ef47c1ab39ba8ffb6a6536d0eb72acdb5a
Author: lijewski <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 9fc7b4111501111b47f63061e7e51082c0ce3d86
Author: lijewski <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 962f3b744e4ff800f3427250353f6ce2fa5b6b52
Author: lijewski <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 15c14c7f8d22b67b65caf93fab7104b13a4678eb
Author: almgren <almgren>
Date:   Fri Aug 25 22:04:03 2006 +0000

    Modified verbosity and removed extraneous argument "solver"

Src/LinearSolvers/F_MG/mg.f90

commit 8dc45d0708e7a10e75a755de26b9a1c9657ab3d6
Author: almgren <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 7023135bad54c17895897b6bdeb7b0184e4d8c14
Author: almgren <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 dcd011f9e06f639582af493c36cb1c2d98cb7468
Author: almgren <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 1c6a329b73b087c100fb012e571a8e8bd0829f60
Author: almgren <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 f9c28f077e40468c775e9b332154ba3f3fd8afec
Author: lijewski <lijewski>
Date:   Thu Aug 24 21:11:50 2006 +0000

    can now choose # of SwapAndTest() calls

Src/C_BaseLib/DistributionMapping.cpp

commit 07b2e2fdd3be92f668f200cf22c0d0c84bac6457
Author: almgren <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 a661d0b33498885aeedebe8b8ec97522b560b443
Author: lijewski <lijewski>
Date:   Mon Aug 21 00:29:45 2006 +0000

    fixed bug in collectdata with do_alltoallv=1

Src/C_BaseLib/FabArray.H

commit b64aa44974e6b208a4e01ed83a64e2329ec2a197
Author: lijewski <lijewski>
Date:   Sat Aug 19 03:47:04 2006 +0000

    didn't have caching quite right

Src/C_BaseLib/FabArray.H

commit 6012f6c8db04be84e235d1e32ee2740eff676c40
Author: lijewski <lijewski>
Date:   Sat Aug 19 03:46:18 2006 +0000

    print out Box when numPts() overflows

Src/C_BaseLib/Box.cpp

commit ccae189de1c996088547b309c42859aa1d4b1e34
Author: almgren <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 a79b78daeb2d8d5ed41a118307a8b48c3e634b99
Author: almgren <almgren>
Date:   Fri Aug 18 22:05:44 2006 +0000

    Small change in formatting.

Src/LinearSolvers/F_MG/mg_cpp.f90

commit ee76cba30582767ea66acef21e73d466b22b1318
Author: almgren <almgren>
Date:   Fri Aug 18 22:04:38 2006 +0000

    Added "save" to mgts declaration.

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 0cb66662056e3a52451ef23f2f275184edb26737
Author: almgren <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 fa761ab908cdc4c0194bda849ae950b9f2417e25
Author: lijewski <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 75fbfaf9462cca20b09a62f06ad6e65ca5945b62
Author: almgren <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 7555ae44ec3c5c059d97e39d3dd5a12d7e5c4176
Author: almgren <almgren>
Date:   Tue Aug 15 19:17:33 2006 +0000

    Remove extra print statements...

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit 7d45480ad234a8a3593da7f713268451d11d481e
Author: almgren <almgren>
Date:   Tue Aug 15 19:16:47 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.f

commit 631f73c51ed2ccf447c880c3cf852d8fcbdadd67
Author: almgren <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 40ebc5ac0abb6fca376b0440feb56872d480f1c4
Author: almgren <almgren>
Date:   Tue Aug 15 19:13:52 2006 +0000

    Modify set_vel_2d...

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit b0a216b84376b1c66fc888ce30e56ca0e78adbb1
Author: almgren <almgren>
Date:   Tue Aug 15 19:13:07 2006 +0000

    Dont need those print statements...

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 527d82abbb7a2641512aee10625937e9311aafa7
Author: lijewski <lijewski>
Date:   Tue Aug 15 19:10:30 2006 +0000

    commented out couple prints

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 2d36dd465e5d9ae735200f65aa6f3b3e1418510f
Author: almgren <almgren>
Date:   Tue Aug 15 05:31:44 2006 +0000

    Fixed diagnostic statements...

Src/LinearSolvers/F_MG/mg_nodal_cpp.f90

commit 54c192b6ff5a5fbc8ddd57020db4cc943e317557
Author: almgren <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 abfc57d2a3da8cef4b3f5d38df359a6ee33668a1
Author: almgren <almgren>
Date:   Tue Aug 15 04:40:00 2006 +0000

    Fixed typo.

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 7f7f8788ef35beba7eb220f4d04eeae3584f39ad
Author: lijewski <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 3448e61489b73f605474ee0abd7b3332487cc14b
Author: almgren <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 88cc62d4822066c22d5630f29749b7936ba119d9
Author: almgren <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 4435398f132d85293e909b6664d41b22ac398180
Author: almgren <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 c20c70dcc51a36b6d02282edb079bed7640b56a2
Author: lijewski <lijewski>
Date:   Tue Aug 15 01:19:15 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 3fc1dde8f4d889c24a65e129cbd0d42087756882
Author: almgren <almgren>
Date:   Mon Aug 14 21:15:03 2006 +0000

    Remove commented line.

Src/LinearSolvers/F_MG/mg.f90

commit 1bd1956e99750d05f121bcdb5bff530919f06742
Author: almgren <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 3348963cfc10f3e8460a2f1235ee43be7651008c
Author: almgren <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 1aad05ff744384ab4b705fb8791152dbaf386ce8
Author: lijewski <lijewski>
Date:   Mon Aug 14 20:22:12 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 9a3195f67a9ee33867ad1bf6df99939ec064546d
Author: almgren <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 6d4ed5cf4049941a8b168a06797b7d8ddc901b8b
Author: almgren <almgren>
Date:   Mon Aug 14 20:06:49 2006 +0000

    Tiny modification in function skewed_q.

Src/LinearSolvers/F_MG/stencil.f90

commit 03a87585197d3acc0ae6b10efb2d091848fede42
Author: almgren <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 0a905080c91e2440cf94293ec22532fb263aa126
Author: lijewski <lijewski>
Date:   Wed Aug 9 18:00:41 2006 +0000

    do NOT do alltoallv() by default

Src/F_BaseLib/multifab.f90

commit 4997b0e71976bc1a40dcfb56e773d8d57612a50b
Author: lijewski <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 bd69519ae725a56fcbfbfadbd5bd33a86ece9353
Author: lijewski <lijewski>
Date:   Wed Aug 9 04:19:38 2006 +0000

    added nocomm flag to fill_boundary & copy

Src/F_BaseLib/multifab.f90

commit e8c52b294de9996b1fe93b64904bf563a3dedcc3
Author: almgren <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 909d22f30b103ffece4b48dc36a415cd8b78ea39
Author: almgren <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 8e602c6afe15b8dc05dabc3314146c9e4c65dbe6
Author: almgren <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 3de7d1f4cfad53efc5b48d73ac1924e55241cf71
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:46:45 2006 +0000

    added mgt_init()

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 85efae0af5a9c5b3601f6389befa22a63445dc38
Author: lijewski <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 839789cd682529d38ee8333adc60cd2f471183ee
Author: lijewski <lijewski>
Date:   Mon Aug 7 18:23:00 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 78f986e1ae4829ee1b59c003df85c372a155f29f
Author: lijewski <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 1eb6e2064d001eaab7363e418ef1e62803be8e0d
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:33:01 2006 +0000

    removed weird embedded comment

Src/F_BaseLib/parallel.f90

commit f96ecbaebd1184df0b2490e73bc1e118d947876d
Author: lijewski <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 69c527c49637869648bee94ad816ecf505a5b455
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:26:18 2006 +0000

    *** empty log message ***

Src/F_BaseLib/mpi.f

commit ba601449e5f67a9004f8686c25080ed5104242cc
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:25:52 2006 +0000

    added save to mgts

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 6a4e3af8e979217801674c6bb6ec7a19af196a1b
Author: lijewski <lijewski>
Date:   Fri Aug 4 22:25:34 2006 +0000

    removed mpi.f

Src/LinearSolvers/F_MG/FParallelMG.mak

commit 2f5a66a282e5d6d8beb077f4edbf8d5308b85657
Author: lijewski <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 f8266e666d24b081033738fba0222a62c063f571
Author: almgren <almgren>
Date:   Thu Aug 3 20:35:06 2006 +0000

    Improve print statements in itsol...

Src/LinearSolvers/F_MG/itsol.f90

commit 42ea98285d322faf2cc9539ef8bfd8f5ae960ebd
Author: almgren <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 fca50edb848e7aeb1b2933fb4860b880a77a2aa1
Author: almgren <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 3ebc7dd038c76bb924aebad8453a76071b4a6252
Author: almgren <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 7578c5bef1c8955e1761e4ff32eeada50a20fc25
Author: almgren <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 1af1c7001c65cfa68a68d8ba28f0119345d98b42
Author: almgren <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 960be32d2983b333861382ecf52339bc4d141403
Author: almgren <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 2a8cb263a63524d64e0c657f2043c1f2bccee41a
Author: almgren <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 c0147cdf0457a779b09dc5b45b7c4fbc21092824
Author: almgren <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 c0d0ddc1468abd3c4f0c8ab915f475d764c325a9
Author: almgren <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 53e004d721899471008e09ee6ea644810a74e885
Author: almgren <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 d00131399d05b6ceccd634cd96bf514667ef3665
Author: lijewski <lijewski>
Date:   Wed Aug 2 21:14:14 2006 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/ba.25600
Src/C_BaseLib/test/tMinCommCosts.cpp
Tests/C_BaseLib/GNUmakefile
Tests/C_BaseLib/ba.25600
Tests/C_BaseLib/tMinCommCosts.cpp

commit 39ba84810b2090720ec773fe26c5ec478a223388
Author: lijewski <lijewski>
Date:   Wed Aug 2 21:13:59 2006 +0000

    speedup of SwapAndTest(); also only call it once.

Src/C_BaseLib/DistributionMapping.cpp

commit 67b3ea75832f7b3cccbdca8f8230510d898fc29a
Author: almgren <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 d4421e2dc98b3d7cb22e283648889309e5b5fbee
Author: almgren <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 93bdb4ba4e1fd77e40d6b5c4d7c9e5be92503ca2
Author: almgren <almgren>
Date:   Wed Aug 2 20:10:56 2006 +0000

    Allow code to reduce order small grids.

Src/LinearSolvers/F_MG/stencil.f90

commit a1bd2a84152c491eddf61a94c20d7c0ba923837f
Author: almgren <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 25123490ad2f9973523983d5fc9aee8a9f7b359b
Author: almgren <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 a271c95052aa4ff70b151a5401d16d622599abce
Author: almgren <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 36b6ca6c23e93b8fc41669245a51c1165a0b8ed8
Author: almgren <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 0a1b208c91b727266c3c3b3ea777f316a9a85924
Author: almgren <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 178ea26945c4c54885b76dbba5fc48be9038abae
Author: almgren <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 6b036cbf54034d92de0e89050549a4454eb778da
Author: almgren <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 0ab20dc382a04dbb01371029e8d1b9117e467ff3
Author: almgren <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 35cb6f0e54af647d6724ec657aaaeedf242987ed
Author: lijewski <lijewski>
Date:   Fri Jul 21 22:16:39 2006 +0000

    cfe3 -> cfe

Tools/C_mk/Make.defs

commit 981f3aa3627010a40f90d789b80fe2d903c361ad
Author: lijewski <lijewski>
Date:   Thu Jul 20 19:54:39 2006 +0000

    comment out timer stuff

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit c47655c332ac55b9d54b6b6f209d7c515eb443fa
Author: almgren <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 0d9da038fb46ca28f389540626267fea88e38a21
Author: lijewski <lijewski>
Date:   Tue Jul 18 03:56:30 2006 +0000

    optimization flags for columbia

Tools/C_mk/Make.Linux

commit 73c6e3016ad5c3e1ce774d04fbf579152f960323
Author: lijewski <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 9ef3aa382957fdd4ef81cf573f213e01e41925dc
Author: lijewski <lijewski>
Date:   Thu Jul 13 21:08:56 2006 +0000

    ipo -> ip for Columbia

Tools/C_mk/Make.Linux

commit 2044330744c8a6f510ea85d5af73aedab29ac303
Author: lijewski <lijewski>
Date:   Fri Jul 7 18:23:26 2006 +0000

    some modest simplification to AddBox() routines

Src/C_BaseLib/FabArray.H

commit 75f1d5cb9a0a96d5680f68d05679bb2deebf3119
Author: almgren <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 d118bb1c3d1e2ce58260dd12f86d0b4a06500240
Author: almgren <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 e991901d1161818ffe2dd4d2360d5bbe7439fe0b
Author: almgren <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 a0d27b942dff86ee38554c517d5b0e1c246fb213
Author: almgren <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 05bb33ffdd01b109041a5f8e8074ec9d9c0c880e
Author: lijewski <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 aeed5c4c6baa6547f99d689cad6b62849ccf3772
Author: lijewski <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 2ae61024442db4fb5bc6a7058cf008a6188cbf53
Author: lijewski <lijewski>
Date:   Tue Jun 27 20:24:52 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 16263e580645ea754263fee3fb3f9f35f3248b75
Author: lijewski <lijewski>
Date:   Tue Jun 27 19:45:04 2006 +0000

    cross stuff now appears to work

Src/F_BaseLib/layout.f90

commit 4484606489e7f230664da1772b253296575b8d68
Author: almgren <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 66e30521e7a8927fb00536084cf1bbfc2c697f20
Author: almgren <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 80a663921431baa15c5489b7f1f8c05793eee8f8
Author: almgren <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 1460fa6fd76f6f35d0e4a5cdac677460e551e920
Author: lijewski <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 66508db9b2ff37ccbf6281e9c6cb6966737d1032
Author: car <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 f5357a32387cc66b78c20bf118474fbeb76866bd
Author: almgren <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 08755d11219c7b0803405e8a915f4ed9b5bc1e65
Author: lijewski <lijewski>
Date:   Thu Jun 22 22:15:46 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit fb63ac5ed1a73d3240c3b3a6ca4901579a8751f9
Author: almgren <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 6daa59fe617d437af377302ed0b557a052f8c709
Author: almgren <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 0b7754bbd8fcb931ef04163e58843de93a70376e
Author: car <car>
Date:   Thu Jun 22 19:28:13 2006 +0000

    closer

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 778dfb439d6b905025e4d47921cc8e0f88de0157
Author: car <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 b8d2cc1428cfa82d4326df80b980ba5a259fe011
Author: car <car>
Date:   Thu Jun 22 19:27:26 2006 +0000

    stop using optional unit

Src/F_BaseLib/layout.f90

commit fdf74ee15d74ae7f587370ac87ecd09693ce8abd
Author: almgren <almgren>
Date:   Thu Jun 22 02:37:12 2006 +0000

    Fix calling sequence for first subroutine.

Src/LinearSolvers/C_NodalMG/amr_real3d.f

commit a32467c6d8e4a72371ab91e7e8e2db124f09b802
Author: car <car>
Date:   Wed Jun 21 22:52:15 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_cpp.f90

commit 74b48fae8e0c2dda5e3b6a213a29bdd7779b0b9e
Author: car <car>
Date:   Wed Jun 21 20:58:25 2006 +0000

    *** empty log message ***

Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp

commit 70aeb74f21068d5e92e1363686e7a9b3bef06224
Author: lijewski <lijewski>
Date:   Wed Jun 21 17:40:12 2006 +0000

    mods for cfe3

Tools/F_mk/GMakeMPI.mak

commit cc0e3aeeeac0a69bcd004c892d50cef29776a621
Author: lijewski <lijewski>
Date:   Tue Jun 20 19:36:38 2006 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 0448c0c2ff12f76728b5d1c5206521a5f8c9cb16
Author: car <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 923c7b8cebebad60cebd5ea760ff52a412ee1eb9
Author: almgren <almgren>
Date:   Tue Jun 20 06:50:14 2006 +0000

    Put abs() around quantities in convergence test.

Src/LinearSolvers/F_MG/itsol.f90

commit 1594d9c525005ac243f940ead27dd36884bda043
Author: lijewski <lijewski>
Date:   Mon Jun 19 21:06:57 2006 +0000

    removed ml_crse_contrib_easy()

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit f08d82bca3134b30d0f5fd953ee7d5da480ff159
Author: lijewski <lijewski>
Date:   Fri Jun 16 22:08:13 2006 +0000

    -Ofast => -O2 for PathScale

Tools/F_mk/GMakedefs.mak

commit b285d554af674d09fb5cd754f837954ec1d92275
Author: lijewski <lijewski>
Date:   Fri Jun 16 21:24:35 2006 +0000

    *** empty log message ***

Src/F_BaseLib/layout.f90

commit ba2e3dcee65e894b909adee5df45b358dafabdba
Author: lijewski <lijewski>
Date:   Fri Jun 16 20:57:52 2006 +0000

    fixed bug in fluxassoc_build

Src/F_BaseLib/layout.f90

commit 5b3dce23ea1d4223066cc3eff62bb7da37270fce
Author: lijewski <lijewski>
Date:   Thu Jun 15 21:44:40 2006 +0000

    sped up fluxassoc_build & copyassoc_build

Src/F_BaseLib/layout.f90

commit 5fcc8f8871de96b51abc3b3a1416ca64caa81ca2
Author: lijewski <lijewski>
Date:   Thu Jun 15 20:34:10 2006 +0000

    removed all 'easy' functions

Src/F_BaseLib/multifab.f90

commit cf0907374307fb9f3f45e99cdf6f3316008388ed
Author: lijewski <lijewski>
Date:   Thu Jun 15 18:12:09 2006 +0000

    added cpy_? functions taking filter arg

Src/F_BaseLib/multifab.f90

commit 51aa0e03ae35c56e93c28f9e732c08112794dfea
Author: lijewski <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 9b47e51199de843cb85af69ac039cdcd8cffe034
Author: lijewski <lijewski>
Date:   Wed Jun 14 22:13:12 2006 +0000

    PGI fixes

Src/F_BaseLib/layout.f90

commit 04cb170d0c1aaeaf96db7e54d3adac19f09c6c1d
Author: lijewski <lijewski>
Date:   Wed Jun 14 22:06:59 2006 +0000

    fixes for PGI

Src/F_BaseLib/knapsack.f90

commit bc29730a71a9f027af4668f99d86bc7649c27c89
Author: lijewski <lijewski>
Date:   Wed Jun 14 20:55:54 2006 +0000

    PGI mods

Tools/F_mk/GMakedefs.mak

commit f17c254f4af153361cc868b8f38e386be9fe08ec
Author: lijewski <lijewski>
Date:   Tue Jun 13 22:20:29 2006 +0000

    initial cut at XT3 (catamount)

Tools/F_mk/GMakedefs.mak

commit 004882171889825a7cfa45e47ba235991273d44a
Author: lijewski <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 f3c606bccec3c38f1c2df0fcac358e581f593e22
Author: lijewski <lijewski>
Date:   Tue Jun 13 20:45:46 2006 +0000

    sped up boxassoc_build

Src/F_BaseLib/layout.f90

commit cf8e75da153c4ae30974e8e38de33ad2fa78bd20
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:23:29 2006 +0000

    speed up of unique_cover

Src/F_BaseLib/layout.f90

commit 8fad29ae3cf95345af2d1f9afd56d00383e55a83
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:00:48 2006 +0000

    added optional sort arg to boxarray_build_l

Src/F_BaseLib/boxarray.f90

commit a255e65ba4bfabf254c5267249607ef45f729e9d
Author: lijewski <lijewski>
Date:   Tue Jun 13 18:00:10 2006 +0000

    *** empty log message ***

Src/F_BaseLib/bndry_reg.f90

commit ea719b9d80d047ab2ef42cedbfb635a0115ebfdd
Author: car <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 0c57d5f6bdfae445cb45bc92c57c9b04db5f40cd
Author: car <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 4c0c739241df01a97503847da9c9329b87c6bc02
Author: car <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 7d173b48a10eb375ee151f25c0b4629fbf3ae89e
Author: lijewski <lijewski>
Date:   Tue Jun 13 16:39:56 2006 +0000

    speed up to build_1

Src/F_BaseLib/bndry_reg.f90

commit 07d117fcaebb51534b5088f5f2d033a1be5220c1
Author: lijewski <lijewski>
Date:   Tue Jun 13 15:41:28 2006 +0000

    bug fix for hash stuff

Src/F_BaseLib/layout.f90

commit 251a709af51d9aaf4459365e87301cb9e62e2bc6
Author: lijewski <lijewski>
Date:   Tue Jun 13 03:43:51 2006 +0000

    added more timers

Src/F_BaseLib/bndry_reg.f90

commit f31e713a82bc89d8fc105bb31beabe48a53b515d
Author: lijewski <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 dac1bc7ab84e0bdf86443e1835e82e58eaa4fa52
Author: lijewski <lijewski>
Date:   Mon Jun 12 22:32:03 2006 +0000

    *** empty log message ***

Src/F_BaseLib/bl_timer.f90

commit 9bf87ab80c1429c570da26938f9efb0472341a6f
Author: lijewski <lijewski>
Date:   Mon Jun 12 22:31:42 2006 +0000

    removed ba_bndry_periodic timer

Src/F_BaseLib/layout.f90

commit 54eec73461e481252e6f9c64e599b3c6862bd12b
Author: lijewski <lijewski>
Date:   Mon Jun 12 21:04:10 2006 +0000

    commented out private statement

Src/F_BaseLib/bl_timer.f90

commit 8ed9119c2bbac9d94360e83ebde7b921f5457a30
Author: lijewski <lijewski>
Date:   Mon Jun 12 17:14:14 2006 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit e046bab253a64fee7617ef586a50b8c8527496a7
Author: almgren <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 c387497128c0bccbf81f59c852ef3bc68c5cda96
Author: almgren <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 11aef1c08276469c573aa7032ab29a964e12e9e9
Author: almgren <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 c7f84c0958a1f551d77939770990655f15ad1243
Author: almgren <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 a3fce98eb4a860133c1a7ef3939e7c55467c515a
Author: lijewski <lijewski>
Date:   Wed Jun 7 22:15:40 2006 +0000

    added verbose flag

Src/F_BaseLib/layout.f90

commit b6cf26110ede30756c9e7719c9d53be52abb1782
Author: lijewski <lijewski>
Date:   Wed Jun 7 22:15:10 2006 +0000

    removed nocomm stuff

Src/F_BaseLib/multifab.f90

commit 6d0e9bdfae4d609e32c98b50e1b4619b36677d35
Author: lijewski <lijewski>
Date:   Wed Jun 7 19:33:11 2006 +0000

    cleanup & simplification

Src/F_BaseLib/multifab.f90

commit db4ef8eb0cf7bb31d27efc666f80aadf7bfdb04d
Author: lijewski <lijewski>
Date:   Tue Jun 6 21:53:33 2006 +0000

    cache stuff for ml_crse_contrib

Src/F_BaseLib/layout.f90

commit 50eb4b91d49c9eb9c29d31612c36450f80d25856
Author: lijewski <lijewski>
Date:   Tue Jun 6 21:53:18 2006 +0000

    stubs for alltoall for integer & logicals

Src/F_BaseLib/parallel_stubs.f90

commit 485a80de2178b340b74cffdaa013c84f1ea5f1e0
Author: lijewski <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 09c52261018c87218836aaea06eea6a85798e8fc
Author: lijewski <lijewski>
Date:   Mon Jun 5 21:39:51 2006 +0000

    added alltoall() for integer data

Src/F_BaseLib/parallel.f90

commit 308c42d8a31c9757d3dbf5566d0bd79c385db88d
Author: car <car>
Date:   Mon Jun 5 21:25:15 2006 +0000

    pointer, intent conflict

Src/F_BaseLib/layout.f90

commit 47c149a00666b35c02fb917b3a8015885d446bf3
Author: lijewski <lijewski>
Date:   Sat Jun 3 02:27:43 2006 +0000

    tiny bit of cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit a611c0db6c9a11659a2658e854a446883bc65749
Author: lijewski <lijewski>
Date:   Fri Jun 2 16:35:49 2006 +0000

    little cleanup

Src/F_BaseLib/bndry_reg.f90

commit 45cbe976ec681c96e989780b71e8265082e513b4
Author: lijewski <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 4344b91cdc8ed386ef66fa389457b54d6be3a089
Author: lijewski <lijewski>
Date:   Thu Jun 1 22:23:20 2006 +0000

    added alltoall()s for MPI_LOGICAL

Src/F_BaseLib/parallel.f90

commit 2ca8a1c492cbad6c365281947afd698624abeeaf
Author: lijewski <lijewski>
Date:   Thu Jun 1 20:18:58 2006 +0000

    made a private member public

Src/F_BaseLib/boxarray.f90

commit 155db2d5ea977ddc18d444e2d74735060340be44
Author: lijewski <lijewski>
Date:   Wed May 31 20:42:49 2006 +0000

    AIX mods

Tools/F_mk/GMakedefs.mak

commit 6ff889b9643c794098becc12779ff4be70fc8a03
Author: lijewski <lijewski>
Date:   Wed May 31 20:16:49 2006 +0000

    tad simplification

Src/LinearSolvers/F_MG/ml_restriction.f90

commit d4e94ecde1f35d60fd2bff9037198ebec8bd4d74
Author: lijewski <lijewski>
Date:   Wed May 31 20:14:45 2006 +0000

    some simplification

Src/F_BaseLib/box.f90
Src/F_BaseLib/layout.f90

commit 87f54c35201327baa0407f2808c1e1122283ac4e
Author: lijewski <lijewski>
Date:   Tue May 30 23:47:55 2006 +0000

    some cleanup

Src/F_BaseLib/box.f90
Src/F_BaseLib/multifab.f90

commit 94d3ac3a67aefe735164822fb45df8b226f2ca5a
Author: lijewski <lijewski>
Date:   Tue May 30 20:07:52 2006 +0000

    more speedups to stencil_nodal_fill

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit c0da1bdea77b6ef1304a529b2a48ea61aedb0896
Author: lijewski <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 250676e60c8a9e11de3a29455d43590fdbc36ec6
Author: lijewski <lijewski>
Date:   Tue May 30 17:47:44 2006 +0000

    added timer to boxarray_add_clean

Src/F_BaseLib/boxarray.f90

commit e8e93fb76a23b931b037d5f7fb7eb564bb589721
Author: lijewski <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 3524c04144af5d85c8ca4880554fea8a189c068b
Author: lijewski <lijewski>
Date:   Sat May 27 17:59:24 2006 +0000

    memory management cleanup; expanded copy_sum()

Src/LinearSolvers/F_MG/ml_restriction.f90

commit d656cc1dcc6077510f2de79f2d4e9bee251878ed
Author: lijewski <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 7a54d66bbee4dfbdf8d3f97f51cdae71090eb3b4
Author: lijewski <lijewski>
Date:   Sat May 27 04:25:05 2006 +0000

    added remote() cycle to internal_sync()

Src/F_BaseLib/multifab.f90

commit f1fd801d3cdd3195f0084cb4d50f71f8691f2281
Author: lijewski <lijewski>
Date:   Sat May 27 03:44:25 2006 +0000

    added timer to internal_sync

Src/F_BaseLib/multifab.f90

commit 7b518a12a4fe0f9534ce8527148305480e1b2312
Author: lijewski <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 94d97f0c7bbec260acffbb34a1a87a76e6bc6796
Author: lijewski <lijewski>
Date:   Fri May 26 23:20:55 2006 +0000

    added a remote() cycle test

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 7a9d38fb00e028d9adf78ddae3ab4272ee705cd3
Author: lijewski <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 e95f365419ac1a60f36f10eb243055dd0c1378d1
Author: car <car>
Date:   Fri May 26 22:41:37 2006 +0000

    don't grow for obmf

Src/F_BaseLib/bndry_reg.f90

commit acc49bd7f6de289a0f04ca2890d8ec2129eed974
Author: lijewski <lijewski>
Date:   Fri May 26 20:42:44 2006 +0000

    changed name of timer

Src/F_BaseLib/layout.f90

commit a4422a93a14e9a59fa4cb0f23217126f2433c654
Author: almgren <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 452892d37cb316a7b4c08985d9e052fa0048b438
Author: lijewski <lijewski>
Date:   Fri May 26 18:23:43 2006 +0000

    removed async stuff & added timers

Src/F_BaseLib/multifab.f90

commit 6b5a20092aee9a4afc4fe7af8596b5541e853422
Author: lijewski <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 11bcaf81ed74570ef32c40026ba168b9d40aa775
Author: car <car>
Date:   Fri May 26 18:11:14 2006 +0000

    unused variable

Src/C_BaseLib/ParmParse.cpp

commit 066cf855bae1c850cff92674417c0e0a77052629
Author: lijewski <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 e29a79b0c06a15fe5a78972310574bc7ff5a4d3f
Author: almgren <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 f718b1fe0d15eae694b1ba5cb45e1f97b89d35d7
Author: lijewski <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 40f94ec0822240936ca5645e61f7873a28db838c
Author: lijewski <lijewski>
Date:   Tue May 23 23:00:33 2006 +0000

    parallelized periodic_add_copy()

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 17a9cb77a577f1e377a2a81ea1904da0ecff78f8
Author: almgren <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 b37d263ee5b8c653a1f040aa229d92095ad9d5ee
Author: almgren <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 44b7d7f44752b5fa41583fa6a00d5760738c5277
Author: almgren <almgren>
Date:   Tue May 23 21:25:44 2006 +0000

    Replace destroy by bl_prof_destroy...

Src/LinearSolvers/F_MG/mg.f90

commit 695b49e347285eca9e23556eea2c91e384aafd10
Author: lijewski <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 ea00b73c1b125ece764f717c74f9d135b02d2b96
Author: lijewski <lijewski>
Date:   Tue May 23 04:40:22 2006 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 55f2c8729bac9a6c7dcfaf97ba5f52cfe0ca2732
Author: lijewski <lijewski>
Date:   Mon May 22 23:20:52 2006 +0000

    intent(out) -> intent(inout)

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 730f8b02ba3a328a553f7806e139d6b73b313e09
Author: lijewski <lijewski>
Date:   Mon May 22 23:20:05 2006 +0000

    wasn't quite right

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 2ce08d5bb2ec08504b1c5c0ff59088ae493a7993
Author: lijewski <lijewski>
Date:   Mon May 22 23:19:20 2006 +0000

     do need to use build_1

Src/LinearSolvers/F_MG/ml_nd.f90

commit b1fb11f73bd96478e5e73d0c16395f43d0ca6020
Author: lijewski <lijewski>
Date:   Mon May 22 20:48:03 2006 +0000

    some cleanup

Src/LinearSolvers/F_MG/ml_nd.f90

commit a679eb206ec8d084ad7e025ec88a714c99c42fbd
Author: almgren <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 14749623548993b87ba05e7de354bb9bbd7465ce
Author: lijewski <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 1f8aac76145a0cd1879c69d183519537a7ec9eca
Author: lijewski <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 750bb1aaa6f3479bb79468696ccaaf441fa7859d
Author: lijewski <lijewski>
Date:   Mon May 22 17:03:22 2006 +0000

    added neede boxarray_destroy()

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit c37da859c9ab40f8369b16d047cc3908e2cb92fe
Author: lijewski <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 6d6df5bb2c026ad617afdf1ad2373934a42b2b53
Author: almgren <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 b9ded1ae3730c58bfb5ba911e2f0dfb248106721
Author: almgren <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 5777cc40b4fcf21c7ed2c84eee2c9a126b9a72da
Author: vince <vince>
Date:   Fri May 19 00:14:09 2006 +0000

    fixed '>' sign.

Src/C_AMRLib/INTERP_3D.F

commit b5f5f139c93777c005446559916f03dbccbb9b9b
Author: car <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 17a5a778bee048919a6a0101035ae00b7def3306
Author: car <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 44ec6604f4f7c705b86a2a791a37da37583d14da
Author: vince <vince>
Date:   Wed May 17 21:34:13 2006 +0000

    gatherv fix for romulus.

Src/C_AMRLib/Amr.cpp

commit 0b3291b0f064d26f4b0d10c19dfde04fc6271d38
Author: almgren <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 7467a081e915e711c7d9e5fe46adc07272cbb9fa
Author: lijewski <lijewski>
Date:   Tue May 16 22:28:37 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_nd.f90

commit 3040b62dbf63e2af3b8760815de83147f32b749c
Author: lijewski <lijewski>
Date:   Tue May 16 21:50:21 2006 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_nd.f90

commit ccbdb6f8d6373e5641b156e4141add27afe53ae5
Author: almgren <almgren>
Date:   Tue May 16 21:24:54 2006 +0000

    Cosmetic changes only, I think.

Src/LinearSolvers/F_MG/mg_restriction.f90

commit c4d1af7eca5e3056835eb0fcb9b550d5191a7532
Author: almgren <almgren>
Date:   Tue May 16 21:21:59 2006 +0000

    Changes necessary for periodic

Src/LinearSolvers/F_MG/ml_interface_stencil.f90

commit 290f605b18e87091bcd7ac0b4e5010a294a23f9a
Author: lijewski <lijewski>
Date:   Tue May 16 21:17:59 2006 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit dd8a57753304a62dfec5ac980643025334c3e4e5
Author: almgren <almgren>
Date:   Tue May 16 21:04:58 2006 +0000

    Changes needed for periodic algorithm.

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 25e147dc498298a7f3a8f342d06ad2d18bd3e971
Author: almgren <almgren>
Date:   Tue May 16 21:03:14 2006 +0000

    Needed correction for periodic.

Src/LinearSolvers/F_MG/ml_util.f90

commit e40f584b151d0b94b48157a40a541ce6ff797dd5
Author: car <car>
Date:   Mon May 15 21:10:35 2006 +0000

    a print function

Src/F_BaseLib/ml_layout.f90

commit d189ec9aec0cea272b1756181a43e6e1ce0cbe6c
Author: car <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 6be5654342348c790b1cdeaf1b0ca3f18e609047
Author: car <car>
Date:   Fri May 12 23:01:14 2006 +0000

    some parallel support

Src/F_BaseLib/bndry_reg.f90

commit de2dde80397b29a837a9f3e6c461c7f46e3bc85e
Author: car <car>
Date:   Fri May 12 23:01:05 2006 +0000

    extra printouts

Src/F_BaseLib/layout.f90

commit 6633bbf816200c3aef896bf31df7948ff0f77b78
Author: car <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 d9bc7a2d171063dbeae04679ea2f1636f15c21d8
Author: car <car>
Date:   Fri May 12 23:00:15 2006 +0000

    nil

Src/F_BaseLib/flux_reg.f90

commit 8ee1fcc2afdbb13af739624720794d6aaab989bd
Author: car <car>
Date:   Fri May 12 22:59:38 2006 +0000

    accomadate  bug in ifort 9.1

Src/F_BaseLib/box.f90

commit 629d0ab59482d6ad25b0e7a35ffb230232265599
Author: car <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 657b12659516a33ed623ae2cb72ab1a9f4d4ea60
Author: lijewski <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 22b2edc112795f274432af4687662509f6707b22
Author: car <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 b4769d4c6cfcf89b18397314846269fc424fb837
Author: car <car>
Date:   Wed May 10 17:47:55 2006 +0000

    maybe a better way to find ifort libraries

Tools/C_mk/Make.defs

commit b688df54ef08ecb827a807b184b55d05bf10870c
Author: lijewski <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 76e7dc3b300c1c14914c688cfce0e6c240f6c845
Author: lijewski <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 0cec6c155a03177e1ac034c6b2ed125c9825fce6
Author: lijewski <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 626cd861237bc4b361a36ad1902598976bf161d2
Author: lijewski <lijewski>
Date:   Fri May 5 18:50:42 2006 +0000

    replaced use of std::pow() with D_TERM()

Src/C_AMRLib/Interpolater.cpp

commit 08a950a6e3c86c58bb48a977fba9ab6c555ff47c
Author: lijewski <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 7ac9871d7c5061c239616c1f1c9fd7b5238196b8
Author: sepp <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 74672198c757aa152c8039aa91de4c5d7e919a55
Author: lijewski <lijewski>
Date:   Wed May 3 18:19:29 2006 +0000

    removed length limit on tokens

Src/C_BaseLib/ParmParse.cpp

commit 387bc9a8972eeb895819439a5346292af7d6844d
Author: lijewski <lijewski>
Date:   Tue May 2 21:25:33 2006 +0000

    *** empty log message ***

Src/C_AMRLib/Amr.cpp

commit 773af358f840598efafaa7e844d0c3bc0eafae12
Author: car <car>
Date:   Tue May 2 18:41:38 2006 +0000

    *** empty log message ***

Src/C_BaseLib/SPECIALIZE_1D.F

commit f4d9676992ba70295a3d0879b8fbfcc439d1b300
Author: lijewski <lijewski>
Date:   Tue May 2 18:01:15 2006 +0000

    no <ONE_D.H>

Src/C_AMRLib/INTERP_1D.F

commit 53693f577dd6b9019bb04f2db6927fa1b2d0cde4
Author: lijewski <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 7302f6fe08a3cf726f478ed66b534d13c903225d
Author: lijewski <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 2e9bd456af2b7dd5e469a08affede8047544da70
Author: lijewski <lijewski>
Date:   Mon May 1 20:26:34 2006 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp
Src/C_BaseLib/Utility.cpp

commit 2bca812703597a66bc76581c79cafba50ec60403
Author: lijewski <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 cec8d87c3fc09c4f2fa40952c34fcaf88a8bb260
Author: car <car>
Date:   Mon May 1 19:19:12 2006 +0000

    not sure i'll need this

Tests/LinearSolvers/F_MG/bc_interp.f90

commit 64912f65e5e4d852a1260ad9eef720b8435b0d6b
Author: lijewski <lijewski>
Date:   Thu Apr 27 21:22:01 2006 +0000

    bug fix

Src/C_BaseLib/FabArray.H

commit b1e912e0f289482517ab201dfc55494bca58c0c9
Author: car <car>
Date:   Thu Apr 27 21:03:08 2006 +0000

    gfortran bug work-around

Src/F_BaseLib/list_box.f90

commit 46293460425014524097e8c76f78e3656185b0f2
Author: car <car>
Date:   Thu Apr 27 21:02:33 2006 +0000

    discriminate between -pg and BL_PROF

Tools/F_mk/GMakedefs.mak

commit 8c0e67fd2c38c071f66a8387b8f4794f4ec50d4d
Author: car <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 e8c42db67f9012cbbd64384c5e72e4fe84cc585a
Author: lijewski <lijewski>
Date:   Mon Apr 24 22:36:31 2006 +0000

    more tweaks to CollectData()

Src/C_BaseLib/FabArray.H

commit f0bc86bf134c3fc3b310ced898ab457515f65422
Author: lijewski <lijewski>
Date:   Mon Apr 24 21:11:03 2006 +0000

    added #ifdef BL_MPI ... #endif

Src/C_BaseLib/FabArray.H

commit 8d1f0b4ee4365ea6e9ac8df036c812a67bfa28b8
Author: lijewski <lijewski>
Date:   Mon Apr 24 17:27:49 2006 +0000

    now uses MPI group operations

Src/C_AMRLib/FluxRegister.cpp

commit 994e649bcad5f289903d0c78e4c2fd00fb8c80fb
Author: car <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 447809865cb0b7edee492b22aadfe03996e30f72
Author: lijewski <lijewski>
Date:   Thu Apr 20 20:15:38 2006 +0000

    slight tweak to CollectData()

Src/C_BaseLib/FabArray.H

commit 48144677369929b588e02fbc823f6bb8343cc658
Author: lijewski <lijewski>
Date:   Thu Apr 20 18:21:41 2006 +0000

    now use group communication protocols in CollectData()

Src/C_BaseLib/FabArray.H

commit 4b67589b1f39b0ab4d4134f03af6ca09215a985e
Author: lijewski <lijewski>
Date:   Wed Apr 19 04:30:29 2006 +0000

    substituted alltoallv() for send()/recv() in ::copy()

Src/C_BaseLib/FabArray.H

commit b881fdab8f7ad685617f2834050e93b376df9ed4
Author: lijewski <lijewski>
Date:   Tue Apr 18 23:19:55 2006 +0000

    wrapped Gatherv()s in BL_MPI_REQUIRE

Src/C_BaseLib/VisMF.cpp

commit e588b78caf304bd2f9ec10ddbe29dd3d74cfcea2
Author: lijewski <lijewski>
Date:   Sat Apr 8 00:01:42 2006 +0000

    use MPI_Gatherv() in VisMF::Write()

Src/C_BaseLib/VisMF.cpp

commit d0bb2a59fe32c29775651ec0a10e5fc66adc9858
Author: lijewski <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 49004c894b41e46ecfd73e9f12195d822e9284f9
Author: car <car>
Date:   Thu Apr 6 13:52:53 2006 +0000

    reformat

Src/F_BaseLib/ml_multifab.f90

commit 9b43671b95c2fde38d69d13d1e4adc283294f3fd
Author: car <car>
Date:   Thu Apr 6 13:52:23 2006 +0000

    lall needed to protect all

Src/F_BaseLib/multifab.f90

commit 788d190390bfff0f25b0d3acf23962b7cf26ce9c
Author: almgren <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 85786394d0784fb354b11f7c28445b09607e6848
Author: almgren <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 4c005cbd52fdbcfffbc749762492f3f618176733
Author: marc <marc>
Date:   Fri Mar 31 22:27:35 2006 +0000

    reduce precision

Src/C_AMRLib/Amr.cpp

commit e08cc248099f0f9d77b6a6df2f51032207c651da
Author: marc <marc>
Date:   Fri Mar 31 21:48:09 2006 +0000

    fix up err in prof statement

Src/C_BaseLib/VisMF.cpp

commit 5106e869b9249ef1483b3d39f7df5fb9af816275
Author: marc <marc>
Date:   Fri Mar 31 21:42:50 2006 +0000

    add a couple of timers

Src/C_BaseLib/VisMF.cpp

commit 2a2f89ba760f71d7b8d10cf5c11a12fdff9ea9dd
Author: vince <vince>
Date:   Thu Mar 30 21:52:12 2006 +0000

    test for old style box.

Src/C_BaseLib/Box.cpp

commit b0c63803e163608335b2d51c2e7cace3fca5435a
Author: car <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 6bb08baedfc5844076f901b78a2805e25564ed10
Author: car <car>
Date:   Mon Mar 20 20:06:28 2006 +0000

    test for ann

Src/F_BaseLib/multifab.f90

commit e3c07c28d21e6af07df42157b91a22de3210c16e
Author: vince <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 8b5bd3fd275f801ae90ba2d33b41c4544e3b3ba0
Author: lijewski <lijewski>
Date:   Mon Mar 13 21:04:11 2006 +0000

    print out distribution with grid log

Src/C_AMRLib/Amr.cpp

commit e9ae19a5701efd68855c0aea4117e87ef3798434
Author: car <car>
Date:   Mon Mar 6 22:23:50 2006 +0000

    forward decls needed

Src/C_BaseLib/FabArray.H

commit 530011db83fdce7510d3875cc02360f74f58ca7e
Author: car <car>
Date:   Mon Mar 6 19:24:44 2006 +0000

    missing declarations

Src/C_BaseLib/VisMF.H

commit 18776ab510aacbaf89a3fe8f514c06400fe9d9cf
Author: lijewski <lijewski>
Date:   Wed Feb 15 22:47:12 2006 +0000

    more tweaking of min comm cost code

Src/C_BaseLib/DistributionMapping.cpp

commit 4453871d01c302ffedc44dbc4f001a98d75282b8
Author: lijewski <lijewski>
Date:   Tue Feb 14 18:56:23 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 8fc0005ac6a6fdf726679004494d8bb482070bd3
Author: car <car>
Date:   Fri Feb 10 22:18:40 2006 +0000

    fewer includes when not profiling

Src/C_BaseLib/Profiler.H

commit 86d7f09893c3261959616714b47852f9e6e1a8f2
Author: car <car>
Date:   Fri Feb 10 22:18:17 2006 +0000

    need string include

Src/LinearSolvers/C_NodalMG/RegType.H

commit cea4b7710ee109333ea9a8687a370920540a7be6
Author: car <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 c1cc3eef684eb5ad17303167e82ad23b97bb7107
Author: car <car>
Date:   Fri Feb 10 17:20:22 2006 +0000

    cleaned up makefile

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 30454112db1b2737300555a3807c741ff8eacdf5
Author: car <car>
Date:   Fri Feb 10 17:10:31 2006 +0000

    naphta

Tools/C_mk/Make.mpi

commit 2eccfd29060cf4a004ce24136da60b394830fa6a
Author: car <car>
Date:   Fri Feb 10 17:10:11 2006 +0000

    BROWSE

Tools/C_mk/Make.rules

commit c9f645efff9018faddad31b872270b1db42431f8
Author: car <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 eeb5406ce0cde91a2d6e19ea1101e7e6845450ab
Author: car <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 552bd7b88ea7ae840588ad4ebac70d5039bad63b
Author: car <car>
Date:   Thu Feb 9 21:40:02 2006 +0000

    iostream...

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 6a446337b3eb4545c14844049fcb620f5d38a894
Author: car <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 326a8ab05a9cb0828b772977549a28069c4f7842
Author: car <car>
Date:   Thu Feb 9 21:08:25 2006 +0000

    include needed for iostream

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 6074e61c0678f1ec9a430a3960f10160f4e09739
Author: car <car>
Date:   Wed Feb 8 21:38:05 2006 +0000

    PGI->BL_PGI

Src/C_BaseLib/Thread.H

commit d642b2362a87850797c09c1837f1bdfdb683b58f
Author: car <car>
Date:   Wed Feb 8 21:37:26 2006 +0000

    wsecond on XT3

Src/C_BaseLib/Utility.cpp

commit 7c30b2a644e43b199886fca6361d46bfc03bb6c3
Author: car <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 ee0ec82a756dbdef563c500a38193137c716e01c
Author: lijewski <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 7547473bf96a9d90911f1dfc2590afee79285ba2
Author: lijewski <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 2cccfc7c8bf08cd14729270b9ef741525ca65f53
Author: lijewski <lijewski>
Date:   Fri Jan 27 23:24:38 2006 +0000

    speedup of MinimizeCommCosts()

Src/C_BaseLib/DistributionMapping.cpp

commit 8626ce13cb3289497aa9d7fe46cdca358b554e26
Author: car <car>
Date:   Thu Jan 26 23:51:58 2006 +0000

    machinefile not needed

Src/LinearSolvers/C_NodalMG/machinefile.mpi

commit 3cf485ca437eca1c237f7ba9a006c25f856f602a
Author: lijewski <lijewski>
Date:   Thu Jan 26 00:12:17 2006 +0000

    zeroed out Execute()

Src/C_BaseLib/Utility.cpp

commit e17d917866600d88ce7a42116a9d531b49bd450f
Author: lijewski <lijewski>
Date:   Thu Jan 26 00:09:26 2006 +0000

    *** empty log message ***

Src/C_BaseLib/Make.package

commit 4f246033f8ce281a136bad6f2e336ba1c7f2ba41
Author: lijewski <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 0692fc8a2a2698a035461b7cba9541405860c996
Author: lijewski <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 a2726e12f493e9e2a833e5a49e81459aa20b66cf
Author: lijewski <lijewski>
Date:   Fri Jan 13 20:26:28 2006 +0000

    use O3 with Fortran & PathScale

Tools/C_mk/Make.Linux

commit 1aef407f6b34649154850f12131bd0994947c129
Author: car <car>
Date:   Tue Jan 10 22:05:28 2006 +0000

    Added another assert.

Src/C_BaseLib/BoxArray.cpp

commit 9534b7eee2384d8d04516da28e5d546f418ed276
Author: car <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 457319502f5724018617c04454aaf54e7610ee41
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:18:48 2006 +0000

    removed some simplify()s

Src/C_AMRLib/Amr.cpp

commit 85d3e377740fece5333ed2f1a399c43e2caa1c81
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:17:24 2006 +0000

    minimize() -> simplify()

Src/C_BaseLib/BoxArray.cpp

commit 62ee9b199de864fab81f0b0cca5a246105bfc763
Author: lijewski <lijewski>
Date:   Mon Jan 9 19:08:58 2006 +0000

    *** empty log message ***

Src/C_BaseLib/test/ba.15784
Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/ba.15784
Tests/C_BaseLib/tBA.cpp

commit 428722fc4cb18e147fe24dd2345b8991ad7df9e4
Author: lijewski <lijewski>
Date:   Mon Jan 9 18:05:16 2006 +0000

    more speedups

Src/C_BaseLib/BoxList.cpp

commit e75c0e252c6d03c1740d6a2b48fa563da4a84312
Author: lijewski <lijewski>
Date:   Mon Jan 9 05:00:30 2006 +0000

    use BoxArray to speed up intersects()

Src/C_AMRLib/Cluster.cpp

commit 28646326b4c7e0b71b98965bd0257fb802fc75a9
Author: lijewski <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 4c65ec305202f2a05f62801d642aa71fa29ebd97
Author: lijewski <lijewski>
Date:   Mon Jan 9 04:23:37 2006 +0000

    speedup of add(BoxList)

Src/C_BaseLib/BoxDomain.cpp

commit 644bbaa4088eea44d382fb41d1ba6cd71b8c690e
Author: lijewski <lijewski>
Date:   Mon Jan 9 02:32:32 2006 +0000

    more profiling

Src/C_BaseLib/BoxDomain.cpp
Src/C_BaseLib/BoxList.cpp

commit ccce47730c5e02d96bd5d98ee9a159b4dcc608c3
Author: lijewski <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 67699f2a769dbe3637e98486f43bad3db2b74ac5
Author: lijewski <lijewski>
Date:   Sat Jan 7 20:35:20 2006 +0000

    think it's finally right

Src/C_BaseLib/BoxList.cpp

commit 8539fb49876b917fa9d9615a1b987d8d2e856888
Author: lijewski <lijewski>
Date:   Sat Jan 7 18:57:30 2006 +0000

    think I fixed complementIn()

Src/C_BaseLib/BoxList.cpp

commit 331938db52e22d5230db3de181fa5744549c3f4a
Author: lijewski <lijewski>
Date:   Sat Jan 7 16:27:05 2006 +0000

    oops, got some weird recursion to work out

Src/C_BaseLib/BoxList.cpp

commit 55b3bc82a1a556516cf16564ced9a8fc4fdd5a9f
Author: lijewski <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 9ecedd012faaec1001731eeecfadd744de98e9ce
Author: lijewski <lijewski>
Date:   Fri Jan 6 22:58:21 2006 +0000

    one complementIn() now calls other

Src/C_BaseLib/BoxList.cpp

commit 5b846a3b683eb5f418554bb97596dc0fa6907dd2
Author: lijewski <lijewski>
Date:   Fri Jan 6 18:47:26 2006 +0000

    efficiency back to .95

Src/C_BaseLib/DistributionMapping.cpp

commit 5b8263b4670781d33a0611afdee9b9b9028579e0
Author: car <car>
Date:   Fri Jan 6 18:46:57 2006 +0000

    newComplementIn

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit e78c272dfb03160c83eb5718c3e7557e8b33cb5c
Author: lijewski <lijewski>
Date:   Fri Jan 6 17:59:40 2006 +0000

    mem improvement for knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit 3a3f907c96c69476e572fd63a535ad6f2f8d55b4
Author: lijewski <lijewski>
Date:   Fri Jan 6 05:34:24 2006 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit f664fb1e785c600c9685b8bdc9d39a4b25cb3581
Author: lijewski <lijewski>
Date:   Thu Jan 5 23:53:10 2006 +0000

    added timers to grid_places()

Src/C_AMRLib/Amr.cpp

commit 5d31405ebdca5a6c0b1bb008913d0ab01b631ee2
Author: lijewski <lijewski>
Date:   Thu Jan 5 23:43:26 2006 +0000

    Print out both initial & final knapsack efficiency.

Src/C_BaseLib/DistributionMapping.cpp

commit 3736beae15daf70bba81487341fa40d23ee815e4
Author: car <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 e3192848b48884708de5ce9effc532eb271ead8c
Author: car <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 e88554e6d5ea05d26b96d5ff2d485e7601d81329
Author: marc <marc>
Date:   Tue Nov 22 22:15:05 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit bf9da3ed3309c484557a7fa475068771c26e9343
Author: marc <marc>
Date:   Tue Nov 22 22:14:47 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 928b9ae779942f0e473faec06d4a4336009cce2f
Author: car <car>
Date:   Fri Nov 18 22:52:16 2005 +0000

    *** empty log message ***

Src/F_BaseLib/ml_multifab.f90

commit 9e84d1b8da2caec801fd6c3f3e4a10fcd1711a0e
Author: car <car>
Date:   Fri Nov 11 18:47:46 2005 +0000

    *** empty log message ***

Src/F_BaseLib/ml_multifab.f90

commit d49f9a2f87f7bfcad4c911f992344b399254268e
Author: car <car>
Date:   Thu Nov 10 23:42:16 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 5d5093fa0dcd456c5351cabe8bc4a3c60c666fd0
Author: car <car>
Date:   Thu Nov 10 23:31:33 2005 +0000

    metis is dead

Src/F_BaseLib/test/GNUmakefile
Tests/F_BaseLib/GNUmakefile

commit 75325bb41e60ab3a209397cd8fe406b4bf72be58
Author: car <car>
Date:   Thu Nov 10 23:24:54 2005 +0000

    PathScale fixes

Tools/F_mk/GMakeMPI.mak
Tools/F_mk/GMakedefs.mak

commit 0338f24eb24be3c6c74e9419d7495adb5cb1689c
Author: car <car>
Date:   Thu Nov 10 23:16:32 2005 +0000

    greenstreet mpi

Tools/F_mk/GMakeMPI.mak

commit 21976547a10bf1f8bec4b93ffdb92c4bbc6702fe
Author: car <car>
Date:   Thu Nov 10 23:11:28 2005 +0000

    farg

Tools/F_mk/GMakeMPI.mak

commit a3f7ed08a14b6488612f254f08c31f1e19f46523
Author: car <car>
Date:   Thu Nov 10 23:03:39 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakeMPI.mak

commit 4f6b2b21a706b6aecb9aa86f961d13664247c8f7
Author: car <car>
Date:   Thu Nov 10 22:51:18 2005 +0000

    farg in extern

Tools/F_mk/GMakeMPI.mak

commit 241edfe4406442a31fde2e3d8d701909358e39f6
Author: car <car>
Date:   Wed Nov 9 17:26:29 2005 +0000

    fix for parallel stats

Src/F_BaseLib/bl_prof.f90

commit f33b01dcce0afabf4579146b9259e97062cca8ef
Author: car <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 2f96daf4f55fc633ef20f38c90831339a09b8690
Author: car <car>
Date:   Tue Nov 8 16:23:57 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit 0f04a10c668624dd932f812dbf232e33d70ae2d4
Author: car <car>
Date:   Tue Nov 8 02:35:19 2005 +0000

    debugging

Src/F_BaseLib/fabio.f90
Src/F_BaseLib/multifab.f90

commit 485c530074d7a5b82016bbdbbccd5116e30e244c
Author: car <car>
Date:   Wed Nov 2 23:49:30 2005 +0000

    barrier after mkdir

Src/F_BaseLib/fabio.f90

commit 7c06096cdfe23ea6780732ad947a787dafcb7937
Author: marc <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 2f30abd1f7b5a0a044a3fab5843225dcb6d7afdb
Author: car <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 f86ed331aaec1bad5919d476e2f53ed7ee3ee9a2
Author: lijewski <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 604cc7acb16173c7376b97a2ea787c4db9d80294
Author: lijewski <lijewski>
Date:   Tue Oct 25 22:13:13 2005 +0000

    some simplification of execute()

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 025b9c21ddf959cdac97a22c43da6dd0193deb3e
Author: car <car>
Date:   Mon Oct 24 22:59:40 2005 +0000

    timers

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit 9ba14a67e310020c39965748a4e50dbec5fdeffe
Author: lijewski <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 60dec598acc821703eb8789810d9df0644784f96
Author: lijewski <lijewski>
Date:   Sat Oct 22 19:41:09 2005 +0000

    default for verbose is now false

Src/C_BaseLib/DistributionMapping.cpp

commit b66bcee76dcf4fa5ab92ada2adc4ed4cd353cfec
Author: lijewski <lijewski>
Date:   Fri Oct 21 03:27:42 2005 +0000

    removed timer & freshened code

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 98e69f27bcf4f5724b9b3da6c8faa59d66e318e7
Author: lijewski <lijewski>
Date:   Thu Oct 20 22:07:38 2005 +0000

    A few more BL_PROFILE calls.

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 9606bcda1aea57e3d5432a3cdf25a8261e40f479
Author: lijewski <lijewski>
Date:   Tue Oct 18 18:19:57 2005 +0000

    some speedups to alloc()

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 60ae9197f1b6129fc7df3c461f805071bfda8529
Author: lijewski <lijewski>
Date:   Tue Oct 18 15:57:34 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit 9c648c3dcb7045a05ffc69734fdf5317b56076d9
Author: lijewski <lijewski>
Date:   Tue Oct 18 15:49:57 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit 161c6ef690941c8d3bb6f05856d63c62df1c7695
Author: car <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 3ba14fddae4d6d74c156e68dc0ecbd56ca1a6e21
Author: lijewski <lijewski>
Date:   Mon Oct 17 18:59:00 2005 +0000

    removed timer from restrict_level()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 9d694618e13175b040dbcfa767f7f275e6a93356
Author: lijewski <lijewski>
Date:   Mon Oct 17 17:50:34 2005 +0000

    merged in intersections()

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 74aed413eae6d4ba962c42164b802abf56047561
Author: lijewski <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 fe56e82d765ce4960b303a30ae0e25e8f2a6398d
Author: lijewski <lijewski>
Date:   Mon Oct 17 03:11:14 2005 +0000

    a working contains(IntVect) using intersections()

Src/C_BaseLib/BoxArray.cpp

commit 55993802af0e7a2d03c36ead0f5d96b39a33e61a
Author: lijewski <lijewski>
Date:   Mon Oct 17 02:21:05 2005 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit bfb68543c14c262d7c6e4badefcad83efaa7b80d
Author: lijewski <lijewski>
Date:   Fri Oct 14 17:22:40 2005 +0000

    more polishing

Src/C_BaseLib/Box.cpp
Src/C_BaseLib/IntVect.cpp

commit 159f9839731b32950fb6772d27a46908c6583650
Author: lijewski <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 c7507d02d5c72968ff55964b1e75ad0dc01b2c54
Author: lijewski <lijewski>
Date:   Thu Oct 13 20:14:16 2005 +0000

    reverting out some previous mods

Src/C_BaseLib/BoxArray.cpp

commit add7016e1df1927893614e51cc60ebb2f3af6426
Author: lijewski <lijewski>
Date:   Thu Oct 13 16:51:04 2005 +0000

    oops

Src/C_BaseLib/BoxArray.cpp

commit 520e14b85b1c22ccabe6a2aaef1e66164d75dff1
Author: lijewski <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 f46d038b59c22cd839c026d41f25da6ef56ff7e8
Author: lijewski <lijewski>
Date:   Wed Oct 12 04:26:31 2005 +0000

    more uses of intersections()

Src/C_BaseLib/BoxArray.cpp

commit ceae194d133d77cec0e6807a0578f49bbe7d4bdc
Author: lijewski <lijewski>
Date:   Wed Oct 12 02:54:55 2005 +0000

    slight speed mods

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 778850471ab1b8880bded59a6b1f0167831b9a06
Author: lijewski <lijewski>
Date:   Tue Oct 11 22:23:26 2005 +0000

    use intersections() in restrict_level()

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 59ef0eda03d91ff23c90c1a5de7e05a0f8def15f
Author: lijewski <lijewski>
Date:   Tue Oct 11 19:07:23 2005 +0000

    additional constructor

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit c6f037aaed1dc8c9fe1c8ce22ac5f057e016616a
Author: car <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 e2d0da6ef5e187303e117647e0e3a97647adb172
Author: lijewski <lijewski>
Date:   Tue Oct 11 17:01:08 2005 +0000

    use minimize() instead of simplify() in removeOverlap()

Src/C_BaseLib/BoxArray.cpp

commit f5ba0ca233d6894e3f49ebce59a48e638d495aec
Author: lijewski <lijewski>
Date:   Tue Oct 11 16:07:18 2005 +0000

    turned off FillPatch verbosity

Src/C_AMRLib/AmrLevel.cpp

commit 60734ebbe19a4fa3e3f83410ad1a514541353cb2
Author: car <car>
Date:   Tue Oct 11 02:32:09 2005 +0000

    added a few timers

Src/LinearSolvers/C_NodalMG/interface.cpp

commit a9e0d23f6e98ef3a8b8bf9c07f18eb2243e2d36e
Author: lijewski <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 e7980b38c352ba93a48cce537ac91d83f1975119
Author: lijewski <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 26eae7c48b17f792c85c3c6534adfdaa303283e5
Author: lijewski <lijewski>
Date:   Mon Oct 10 21:00:23 2005 +0000

    added timer to FillPatch::Initialize()

Src/C_AMRLib/AmrLevel.cpp

commit 485fd8f86738b1fe34cc1bc1710e00a1822353fe
Author: car <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 a3689e3ebb5ef6b73944d66ebf8f6759717c2914
Author: car <car>
Date:   Mon Oct 10 18:01:23 2005 +0000

    help find g77 library

Tools/C_mk/Make.defs

commit bb9748e767d7ba18a9b4db414ae1a59956074976
Author: lijewski <lijewski>
Date:   Sun Oct 9 03:08:33 2005 +0000

    inlined min()/max()

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit 5777ca53ff2862595f3b2dbbeec79cc5f3144ef9
Author: lijewski <lijewski>
Date:   Sun Oct 9 02:23:00 2005 +0000

    fix to intersections() for empty BoxArrays

Src/C_BaseLib/BoxArray.cpp

commit d751a18a9aeb92ea1cdeedfc6aa0421a81ac4deb
Author: lijewski <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 f7bde0f4f9ece6220549db87e816ea79f807357c
Author: lijewski <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 c98315b5403438e4295b33163e1cfbcec2644ba4
Author: lijewski <lijewski>
Date:   Sat Oct 8 01:54:46 2005 +0000

    added GetBndryCells()

Src/C_BaseLib/test/tBA.cpp
Tests/C_BaseLib/tBA.cpp

commit 6be21e8ec0a1c8729001b04e3ddade8ecfaca5ef
Author: lijewski <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 9cc51bacbfaaba3afbfd12c1be3a1e0ab5ea0615
Author: lijewski <lijewski>
Date:   Fri Oct 7 21:50:29 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxArray.cpp

commit 2ac8cd73e77c7d7b3114e3db37a827268e97a78a
Author: car <car>
Date:   Fri Oct 7 17:02:00 2005 +0000

    profiler

Src/C_AMRLib/TagBox.cpp
Src/C_BaseLib/Geometry.cpp

commit 5a896d7393c7a75574ee9001045682198c458f60
Author: lijewski <lijewski>
Date:   Fri Oct 7 17:01:13 2005 +0000

    now use intersections() stuff in one AddBox()

Src/C_BaseLib/FabArray.H

commit 5b570efb90701d0ad19eed8b15a6f04635930b1e
Author: lijewski <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 ddfcd8ca4286cd6d8f5d2d4e4f6e047da744a6d3
Author: lijewski <lijewski>
Date:   Thu Oct 6 17:26:16 2005 +0000

    now use intersections() in CrseInit(Fab)

Src/C_AMRLib/FluxRegister.cpp

commit feceeef67263287618efc14e1b9098b016b958fa
Author: car <car>
Date:   Wed Oct 5 22:45:56 2005 +0000

    timers

Src/C_AMRLib/FluxRegister.cpp

commit d6e915ffdc97e3e9842cefc5dc4b5ac598c1bf13
Author: lijewski <lijewski>
Date:   Wed Oct 5 21:44:12 2005 +0000

    use intersections() in FillBoundary

Src/C_BaseLib/MultiFab.cpp

commit 55070c604ff233b21b3045ab9572b9f3654c9c33
Author: lijewski <lijewski>
Date:   Wed Oct 5 21:22:14 2005 +0000

    use intersections() in copy()

Src/C_BaseLib/FabArray.H

commit 4690e464cddbfdc74c0ac7e0f9a0ebb007dffd53
Author: car <car>
Date:   Wed Oct 5 20:28:48 2005 +0000

    pathscale wrong about shared(filter)

Src/F_BaseLib/multifab.f90

commit d19c79e4f3b7115dc818699479fc8d227c7afef4
Author: car <car>
Date:   Wed Oct 5 20:25:05 2005 +0000

    shared fcns?

Src/F_BaseLib/multifab.f90

commit 55bf3830699b71b279fc1be42b0cf25ba602392f
Author: car <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 3fe615ad2b2667fbf0ed587331285e16c579c40a
Author: lijewski <lijewski>
Date:   Wed Oct 5 19:25:04 2005 +0000

    added intersections()

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 617c182ba62e8ea2462d6c83b70dde1d2b2a56d5
Author: lijewski <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 671658df2244430dd365816258f0f253ebf4476c
Author: car <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 1065e15684bf6268956c87c4d0ac685de5a1fada
Author: car <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 667a7db87854552ef4d37ff7727ed67288267918
Author: lijewski <lijewski>
Date:   Tue Oct 4 17:33:05 2005 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit e7ed9d4d718bcbb82ad0a1b96411eedf3b5812c3
Author: lijewski <lijewski>
Date:   Fri Sep 30 19:26:42 2005 +0000

    *** empty log message ***

Src/C_BaseLib/bl_flush.f

commit bb78205e3d0ee2a9324872bd751bc1b9d80debe3
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:41:56 2005 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.cpp

commit c9b0649d698993190a1ec2b6d79bdfe9ad8d6978
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:41:39 2005 +0000

    add flush(6)

Src/C_BaseLib/BLBoxLib_F.f

commit 11be5d5b12a8b4b5459e3db04671984be5b8a3e2
Author: lijewski <lijewski>
Date:   Fri Sep 30 17:07:58 2005 +0000

    add FORTRAN to bl_ output strings

Src/C_BaseLib/BoxLib.cpp

commit 63e1db7e8ee9922e023f15a0407a2241f7233a8a
Author: car <car>
Date:   Fri Sep 30 16:50:20 2005 +0000

    cerr message on abort

Src/C_AMRLib/StateData.cpp

commit 58743341897a2204d8f0de800fa3e7c9a94d862b
Author: car <car>
Date:   Fri Sep 30 16:47:39 2005 +0000

    cout --> cerr

Src/C_AMRLib/StationData.cpp

commit d39916944f126c0a7d792fa40eba61e3411bf414
Author: car <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 929d8cdb0fe568c68c1c42a67e2d23b93b8a6da7
Author: car <car>
Date:   Thu Sep 29 15:55:17 2005 +0000

    timer

Src/LinearSolvers/F_MG/stencil.f90

commit 4c7907e51c230e3b5c9cc524bd53ba37f8f58cd5
Author: car <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 7a938e549024eacaffa8e50a0642c52034e41950
Author: car <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 7de62d6652da770938dda4ecad53b30901f9308a
Author: car <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 78571d1109d9dfcf47b37b0bef8821a39c392156
Author: car <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 2ea338d1559f99ee33ae2a50deaf0e8a44955be6
Author: car <car>
Date:   Tue Sep 27 16:42:11 2005 +0000

    gcc 4.0 support

Tools/C_mk/Make.defs

commit 587aff0e39ca472b367f217aedc934551eb0226d
Author: car <car>
Date:   Tue Sep 27 16:40:09 2005 +0000

    *** empty log message ***

Src/C_BaseLib/.cvsignore

commit a3b5a6619defc8f00afadfa9c4413239c906b204
Author: lijewski <lijewski>
Date:   Fri Sep 23 22:46:07 2005 +0000

    added do_alltoallv stuff to copy()

Src/F_BaseLib/multifab.f90

commit 66678579fbddf910b1f8c4c5ff041eecb1696d78
Author: car <car>
Date:   Fri Sep 23 15:40:07 2005 +0000

    max min and count

Src/F_BaseLib/bl_prof.f90

commit 70d6c10b855328537a256b43bbe9b92ade3dc006
Author: car <car>
Date:   Thu Sep 22 22:39:43 2005 +0000

    remove testing smoothers

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 765b6e0c93701111004b1b9d2aa9c874600c1914
Author: lijewski <lijewski>
Date:   Thu Sep 22 22:23:40 2005 +0000

    optimized copyassoc_build()

Src/F_BaseLib/layout.f90

commit 961934b61096b7ac755099ec3f898c07a84c1e1a
Author: car <car>
Date:   Thu Sep 22 22:00:23 2005 +0000

    back off the fancy stuff

Src/LinearSolvers/F_MG/mg_smoother.f90

commit a1e53638281eb7ac0c0b2daa2063bf1eb6b3135b
Author: car <car>
Date:   Thu Sep 22 20:00:01 2005 +0000

    in serial, use cpu time

Src/F_BaseLib/bl_prof.f90

commit 85fec4b34caf6f6431d89eb408049ee54d127e63
Author: car <car>
Date:   Thu Sep 22 19:59:05 2005 +0000

    new smoother, doesn't seem faster

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 1f8e44f021da3ed2fd1eba075654c113f0aaa72b
Author: car <car>
Date:   Wed Sep 21 23:01:13 2005 +0000

    if not parallel dont reprise numbers

Src/F_BaseLib/bl_prof.f90

commit 23cbbfb3d8708c42c7a97d6e0ac976c5653ce5bc
Author: car <car>
Date:   Wed Sep 21 20:11:28 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90

commit 3052f25763a3200970e80014f3a5e8fb8c574353
Author: car <car>
Date:   Wed Sep 21 19:52:13 2005 +0000

    finally fixed

Src/F_BaseLib/bl_prof.f90

commit 6fd9a71b258ae3af082b575ef04231cfae455082
Author: lijewski <lijewski>
Date:   Wed Sep 21 19:34:53 2005 +0000

    hueristic for chunksize

Src/F_BaseLib/layout.f90

commit feccecbc55c0c1040e47e445046c8f75956eed17
Author: car <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 c923e338e339c38deb4a87c5c2c9a22de9858007
Author: car <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 bd4580ef39679e3647b6692cd2bdb7b121215a8c
Author: lijewski <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 4f8a78c3c42b2a71cf371383524733cecebae192
Author: car <car>
Date:   Wed Sep 21 16:22:13 2005 +0000

    no more do_atav

Src/F_BaseLib/multifab.f90

commit a8f59503e430c2615d29391db21ad7fc8bfdb35d
Author: car <car>
Date:   Wed Sep 21 01:01:21 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_prof.f90

commit 7b3bfe47b001bedba3db599c33566692542885aa
Author: car <car>
Date:   Wed Sep 21 00:27:01 2005 +0000

    fix for reduction

Src/F_BaseLib/bl_prof.f90

commit 0d1ec18d3950f3d84d9e13c0f48f67ad1c44bd03
Author: lijewski <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 263b6ddabc02a93e66b7594521956f09dff80932
Author: car <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 4dbf74b94aff5cd3f0f58b8f930320184f580fa6
Author: car <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 0454f9cf1cb698662494f0f61662e2834f15bce7
Author: lijewski <lijewski>
Date:   Tue Sep 20 16:40:30 2005 +0000

    added timer around boxassoc_build

Src/F_BaseLib/layout.f90

commit 4e652cebf9eb307dc3aef2c298dd7f572d609244
Author: car <car>
Date:   Tue Sep 20 00:09:29 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 24050f9e80a91b3f40226886d443371d274a6a1d
Author: car <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 d6baff9f26984336588a1e2ec75393494e0f2f32
Author: almgren <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 bc3943e1d5e257f3f7aaf365b0e89bd7be7c3f0b
Author: car <car>
Date:   Mon Sep 19 20:46:33 2005 +0000

    norm profiling

Src/F_BaseLib/multifab.f90

commit dd7be6d39ca3b41cd7e7bf7527ee8aa2b5330014
Author: car <car>
Date:   Mon Sep 19 19:50:24 2005 +0000

    summary stats

Src/F_BaseLib/bl_prof.f90

commit b4524c5e33a2044eca7ecef192aac1fc27860b14
Author: car <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 5a2691f1e7bb52980adf294ed25995e5125f5d86
Author: car <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 927408cd9b6a0053ceb0ccffbb5646f9e2707bd5
Author: car <car>
Date:   Sun Sep 18 21:52:59 2005 +0000

    profiler

Src/F_BaseLib/bl_prof.f90
Src/F_BaseLib/multifab.f90

commit 8b6839886ad1f3b7e4bca89f901ba47e0bd3a498
Author: car <car>
Date:   Sun Sep 18 17:54:00 2005 +0000

    good first cut of bl_prof

Src/F_BaseLib/bl_prof.f90

commit 6f5043c036d66482b2ec0f69c16e93ebc9ddbbf5
Author: car <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 f1bdca5672f8cc7452e3d16a0264303088079345
Author: car <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 9af7b6e6f49a26a843c54c3968be9075ceb2f60a
Author: car <car>
Date:   Sat Sep 17 13:58:41 2005 +0000

    tweak for reduce

Src/F_BaseLib/bl_timer.f90

commit dd6fa0e2bda37020a0b49bb8d3ecd6c41adc56b8
Author: car <car>
Date:   Sat Sep 17 13:57:58 2005 +0000

    mg_tower_print

Src/LinearSolvers/F_MG/mg.f90

commit d361a1ffb369e8b9dfdeb62f53ae7f9bed5f4d6f
Author: almgren <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 60d8a86e6b81e784fbe904c2bf1f225172940106
Author: lijewski <lijewski>
Date:   Mon Sep 12 16:14:05 2005 +0000

    turn off minimize comm costs stuff

Src/C_BaseLib/DistributionMapping.cpp

commit b6219af8aba53dd63a69708cf39d67a79fd20ac3
Author: car <car>
Date:   Mon Sep 12 14:12:19 2005 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak

commit c5e86cc321ed54fd2ad2770803e38cedc9938fff
Author: car <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 2655e1ec9dd1fef746f11dbe0275c3c33d5897db
Author: almgren <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 42a2aef77695ab9789316f4d2a351ea2a6989d74
Author: car <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 eafd68222209c46f1584bda0e2a62713eb9a40a8
Author: jbb <jbb>
Date:   Wed Sep 7 21:13:00 2005 +0000

    Oops - typo in previous INTERP_2D.F

Src/C_AMRLib/INTERP_2D.F

commit 90836f771cfeda8d9f6034a15d6c54d8351d1da8
Author: jbb <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 817b8121a26f90473c75a06063ad69195ab4666b
Author: car <car>
Date:   Wed Sep 7 19:22:31 2005 +0000

    added marc's dsp generating code

Tools/C_mk/Make.rules

commit 25250fae65997f0156bb9dc36281dac09a3a8e93
Author: car <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 d836faba212d43c5dee901fd1f304fba6c3cc00a
Author: car <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 30b9fcfc71e9e580de2f93c6dfd29f05f2c4d24b
Author: car <car>
Date:   Wed Sep 7 17:02:14 2005 +0000

    *** empty log message ***

Tools/C_scripts/moddep.pl

commit 2043e8569c0e008378a4eee4142cefbc2a44ab20
Author: car <car>
Date:   Tue Sep 6 22:52:23 2005 +0000

    Intel9 support

Tools/F_mk/GMakedefs.mak

commit c9df1f7d77f0c60e609a22473318eedfa94de0f9
Author: car <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 4411172eb1105e4fbe57b895719c13d7c67c4355
Author: car <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 f544a43fec109c2a933c597f7a544d8c23016c46
Author: car <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 26a4099fc1234e5fb3cad173237bf0a4b30fab83
Author: almgren <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 4aef65bc74727e1b7d5e3e88537edc232d509b9c
Author: almgren <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 631177770fbfb013da506dfdf5af2380ffa849a8
Author: almgren <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 c219663a4d3549ae312bf88a33a9ef12d04e4fc3
Author: car <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 0668c523f27259fac9317132c6b96ff646ef9c1e
Author: lijewski <lijewski>
Date:   Mon Aug 29 16:27:16 2005 +0000

    amr.restart=init -> call initialInit() not restart()

Src/C_AMRLib/Amr.cpp

commit 59a58e85e6232e08a06dfa4dee0066cfee614f71
Author: car <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 a254a1df524494bcf015d84c1d6c945b6938a947
Author: car <car>
Date:   Wed Aug 24 20:22:46 2005 +0000

    added cluster_2d.f90, temporarily

Src/F_BaseLib/GPackage.mak

commit 3b06f5fccd9264590caf3c5bd86f1556ba46c2bb
Author: car <car>
Date:   Wed Aug 24 16:41:02 2005 +0000

    one more check for underflow

Src/LinearSolvers/F_MG/itsol.f90

commit 4b914088e4f2dfd46819159456787155a41cacbe
Author: car <car>
Date:   Tue Aug 23 19:02:29 2005 +0000

    better error control

Src/LinearSolvers/F_MG/itsol.f90

commit dadf98f49fd09ae1e7b5d435bfd627f5de57644e
Author: car <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 b8da19766396ac1aaec3f4f377fa2abe94878f66
Author: car <car>
Date:   Mon Aug 22 19:19:46 2005 +0000

    remove c++ wrapper from compilation

Src/LinearSolvers/F_MG/GPackage.mak

commit 9a574c876705651516270dc4e66fb2c21f11fdd2
Author: car <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 00667e2e676da44f32344af8a2d30a14bc9c0939
Author: car <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 de838ebb83bad71e81dfcfd14eeaafeb1ee809a0
Author: car <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 d55aceced93c056b381b71ded94ed819409c73e6
Author: car <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 c5e904da10db1005378915057746358048355f58
Author: car <car>
Date:   Sat Aug 20 16:39:57 2005 +0000

    cluster should be debugged

Src/F_BaseLib/cluster.f90

commit c673065973778d4a1e0d5fafcbb3c9204061bd4b
Author: almgren <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 a1cc8f64131586f52f7bc42e35d159e2c731c0ca
Author: car <car>
Date:   Fri Aug 19 23:08:32 2005 +0000

    tweaks for mpi

Tools/F_mk/GMakedefs.mak

commit 285e718277e0220b0098236dc647619d0f36a3be
Author: car <car>
Date:   Fri Aug 19 23:08:08 2005 +0000

    get_boxarray

Src/LinearSolvers/F_MG/mg.f90

commit 530c3a343bb73e727419435293f29b8a653b8f8b
Author: car <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 02f06319a5676078691e6acbcadce0f1d9a3fb66
Author: car <car>
Date:   Wed Aug 17 13:29:56 2005 +0000

    *** empty log message ***

Src/F_BaseLib/fab.f90
Src/F_BaseLib/multifab.f90

commit e31f5e9fd5287f54a7d4cd40eb98eef061f02096
Author: car <car>
Date:   Sat Aug 13 15:47:54 2005 +0000

    missed some

Src/F_BaseLib/parallel.f90

commit 28862e8e3634e4ad6510b8e6ca545e76045492d9
Author: car <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 204eda4433ca10dcf15d69d28d239666e86089b5
Author: car <car>
Date:   Fri Aug 12 17:21:57 2005 +0000

    oops

Src/F_BaseLib/parallel_stubs.f90

commit 526b15c0165ad28a5f05fe4a9cb302254daaaccf
Author: car <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 4cea41f4325c6b0e05844313a4dd945c62644448
Author: car <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 fe66adad57bfa80ec52bd9c6bcf34456c09dd3c3
Author: car <car>
Date:   Wed Aug 3 20:25:32 2005 +0000

    oops

Src/F_BaseLib/ml_layout.f90

commit 19a9fdb7460b2f80ba20a0eb838361abdff16d62
Author: car <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 d9a0ca35309acf5ee271782ed5902053623164d9
Author: car <car>
Date:   Wed Aug 3 14:43:09 2005 +0000

    ml_layout

Src/F_BaseLib/layout.f90
Src/F_BaseLib/ml_layout.f90

commit b8d1e1b3c2a09717501203ea3bf879335363c4e0
Author: car <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 9d3952f9f9a67ce14786891b3fecd645263dbea8
Author: almgren <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 dfa0927c62f265e9bab4fb3f1a8094661d5e5440
Author: car <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 60fa7a7318361f5be2f0d67134cc968ab4fb45e8
Author: car <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 d32ea0d09bdf62f6d45f4f7bcfcdfa2ee984e956
Author: almgren <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 de7d04559f0b3dabb7c98ae231b6dfec9b7aa746
Author: almgren <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 b78182062bfe83a57d3bfdcff09801c506d09edd
Author: almgren <almgren>
Date:   Wed Jul 27 20:26:09 2005 +0000

    Index bug...

Src/F_BaseLib/cluster.f90

commit 814c5204ea1724cd28455a4d7e5f0ef4b3542a1b
Author: car <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 9f4c3c2075932baab80cd349faa6a3ec21350cdf
Author: car <car>
Date:   Tue Jul 26 16:48:37 2005 +0000

    lets build boxarrays out of list_boxes

Src/F_BaseLib/boxarray.f90

commit ff37d6cbf42ca94c2dfd6d6c8b6d8a7625080544
Author: car <car>
Date:   Thu Jul 21 18:13:13 2005 +0000

    complex fabs

Src/F_BaseLib/fab.f90

commit f66d7b6d50b1a0b00c1cdb6a963a425663121320
Author: lijewski <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 6d302c95ff1126d853f8a6e015a22e790e6f15ba
Author: car <car>
Date:   Mon Jul 4 23:12:22 2005 +0000

    *** empty log message ***

Src/F_BaseLib/bl_types.f90

commit d30a62674ddfce953ae6c20765944fa17e0440d9
Author: car <car>
Date:   Mon Jul 4 22:52:01 2005 +0000

    endian test

Src/F_BaseLib/bl_types.f90

commit d69fa57d9d69f6bd1c198eb50d826d0d948a02c9
Author: car <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 fd0648d398f1f68f10034e71e332b31c03d8bde4
Author: lijewski <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 71192f64f0a8c34e7ffc4338b390b9dd9d89a86e
Author: lijewski <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 7a6d871f6e9935d6641fa8bb229ffad5aee340da
Author: car <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 927e32a60cafcca76df11f65dd063ed2dd4a0414
Author: car <car>
Date:   Fri Jun 17 17:08:31 2005 +0000

    OMP fix

Src/LinearSolvers/F_MG/stencil.f90

commit 921c5509c171a067a91a89c33d69443924ad4c4c
Author: car <car>
Date:   Fri Jun 17 02:03:28 2005 +0000

    new mech for intrisics

Tools/F_mk/GMakedefs.mak

commit 8441fd9c5bc6f49a97c31fcf02da8f9f3f8d861e
Author: car <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 9c50fb92de721f323d5b7553ec98e4e2aff57b42
Author: car <car>
Date:   Tue Jun 14 20:00:24 2005 +0000

    support for Intel 9

Tools/F_mk/GMakedefs.mak

commit 3a1b997e7115239cf44e0d2ea751605cf42afc58
Author: car <car>
Date:   Tue Jun 14 16:30:11 2005 +0000

    not need external on iagc

Src/F_BaseLib/f2kcli.f90

commit 162353772f53d9587d99ec6c7d3465bf92a29f57
Author: car <car>
Date:   Tue Jun 14 16:23:08 2005 +0000

    Lahey checking

Tools/C_mk/Make.Linux

commit eb979c2dec93a2639c8d7f2fb7b38ff44533fba8
Author: car <car>
Date:   Tue Jun 14 16:22:54 2005 +0000

    icpc/ifort version 9

Tools/C_mk/Make.defs

commit d16bb0a168a56f11a57bedb51a0fe61595791530
Author: car <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 4c2ee23d86089a9757daef8e63aa7cfc9d5aaea6
Author: lijewski <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 bbc6cd6634d9e0558523ba99049eb377c694d9ca
Author: almgren <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 03e220b804d3046ea473de194bf255a84b3ff139
Author: almgren <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 f569dff58c5bd2d954fc9c4ad77eb9d764f0ce3e
Author: lijewski <lijewski>
Date:   Wed Jun 8 21:50:04 2005 +0000

    ml_nodal_restriction is now parallelized

Src/LinearSolvers/F_MG/ml_restriction.f90

commit b7e3d074d91a3256da05e1099e4bd30cc47768ab
Author: lijewski <lijewski>
Date:   Wed Jun 8 17:26:00 2005 +0000

    added filtering ability to copy routines

Src/F_BaseLib/multifab.f90

commit e3e7929dbd98f0f42c627fda62486494c17fa29c
Author: almgren <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 c367a49cad316882fc9359267189074cf6077dff
Author: lijewski <lijewski>
Date:   Tue Jun 7 18:09:53 2005 +0000

    added nodal zero routines

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 3181d81999d05c74c3818d6a557691bd2cb1c036
Author: almgren <almgren>
Date:   Tue Jun 7 18:03:31 2005 +0000

    Formatting...

Src/LinearSolvers/F_MG/ml_nd.f90

commit b7c3d86f22bdfe8136738f55b665f8c19b595223
Author: almgren <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 f32cf7fda9fcc194e2710c514123f84f98e01375
Author: car <car>
Date:   Mon Jun 6 18:17:43 2005 +0000

    lnc

Src/F_BaseLib/multifab.f90

commit 8cb459eac46f8a11675c86201727f0f64743c8a9
Author: almgren <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 6b086d4f401ce69ecb93a41900375d425daeeb51
Author: almgren <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 8723b24e6e0e49b213d4fa74a693c8dbba427ba8
Author: lijewski <lijewski>
Date:   Fri Jun 3 22:49:05 2005 +0000

    added error checks in dataptr routines

Src/F_BaseLib/fab.f90

commit 163f4b797020481121287bc5fff7d56f4546aa1e
Author: lijewski <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 a1285b9aabcbb8531dabc011f3acc92c0f518dfe
Author: lijewski <lijewski>
Date:   Fri Jun 3 19:39:49 2005 +0000

    parallelized ml_edge_restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 325ae184f8da47ef5472d8fb83f882c46d003caa
Author: lijewski <lijewski>
Date:   Fri Jun 3 19:16:51 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/ml_restriction.f90

commit bd4028b9211fde9e45e32043d1ade0a99af3b703
Author: lijewski <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 039d86a03e06a52e2185748fbcc9ffd227b218f3
Author: almgren <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 8d8eaa4675690034d4fbd2263c9b6f249891595c
Author: lijewski <lijewski>
Date:   Thu Jun 2 20:35:36 2005 +0000

    a little cleanup

Src/LinearSolvers/F_MG/mg_prolongation.f90

commit b15676667bd11efe5269f4e4177cf0d8a4f5c2bf
Author: lijewski <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 b7e5c97eeaa13a9d723b6ac7e12ea1e7f8169732
Author: vince <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 1603587bc1ec13d3f5fbf06b2a20ac64422b4ac3
Author: lijewski <lijewski>
Date:   Wed Jun 1 22:28:52 2005 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90

commit 374b8c75a8cfa03e0ae139d7ead705bd10f907f6
Author: car <car>
Date:   Wed Jun 1 21:40:35 2005 +0000

    should read ml_boxarray with != rr properly

Src/F_BaseLib/box_util.f90

commit 99101c835143c68b7a291b1eda259809dfbafd06
Author: almgren <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 eebe9672e9ca65963415b8342e0dbb1c037964ad
Author: lijewski <lijewski>
Date:   Wed Jun 1 20:14:38 2005 +0000

    parallelized ml_prolongation

Src/LinearSolvers/F_MG/ml_prolongation.f90

commit 7b26e9a7a741300b166cf6e539556a8ee188b011
Author: lijewski <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 b86de26ea7a09adf34ac1163ff4c12fdd261d0d0
Author: lijewski <lijewski>
Date:   Tue May 31 21:38:19 2005 +0000

    some cleanup

Src/LinearSolvers/F_MG/mg_restriction.f90

commit d0e19f050874e96a6b99edb7ff087072295371e9
Author: lijewski <lijewski>
Date:   Tue May 31 21:38:04 2005 +0000

    parallelized cell-centered restriction

Src/LinearSolvers/F_MG/ml_restriction.f90

commit 7d4d5b6cdadde97ef102ebc3eb0fa03b55579175
Author: marc <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 3af3a3bb3b30e34ccddecc2fdf636136e4ecf146
Author: car <car>
Date:   Tue May 31 17:21:44 2005 +0000

    more ignorance

Tests/LinearSolvers/F_MG/.cvsignore

commit b32d15a42d1c585669c3422e17804ffc55b3b5d5
Author: car <car>
Date:   Fri May 27 21:59:23 2005 +0000

    strengthen optimization on non amd systems

Tools/F_mk/GMakedefs.mak

commit 72aefc02e5fa390578929e2b61e3d2820ec0e871
Author: car <car>
Date:   Fri May 27 21:58:11 2005 +0000

    BC_UNDEF

Src/F_BaseLib/bc.f90

commit 8be2ac04ed1ce6271a1338679337dfc2c28bffff
Author: car <car>
Date:   Fri May 27 21:57:21 2005 +0000

    memory leak fix; pointer->allocatable

Src/LinearSolvers/F_MG/ml_nd.f90

commit b5d30c99582bd70aa4336bc5f4044b795c8ec6cd
Author: lijewski <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 78a75b4b6addbcb8ba53fb8f881fa3dfae2a4611
Author: car <car>
Date:   Thu May 26 16:42:02 2005 +0000

    memory leak

Src/LinearSolvers/F_MG/ml_cc.f90

commit ba7ee51884eadb3c0698d124eb7ef903bf32bee0
Author: almgren <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 03526f92ca7ab9ba00e038e983541919e8c5b16a
Author: colella <colella>
Date:   Wed May 25 18:29:23 2005 +0000

    Comment out pretty_print.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 1d5314618ec382ceb4a4d94e75abdf27c9cd9655
Author: lijewski <lijewski>
Date:   Tue May 24 22:31:22 2005 +0000

    added the_copyassoc_head

Src/F_BaseLib/layout.f90

commit 3eda9853c40be9ef03342e05498b1a882616d47b
Author: lijewski <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 bd740614943c8cb98365721cc39a6146556006ce
Author: lijewski <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 9e76bd20d1810674e5c7c81df65096a0d6b2ba62
Author: lijewski <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 5b82f49dd8d823215ca0a681f69a45877b6e0179
Author: lijewski <lijewski>
Date:   Fri May 20 21:30:11 2005 +0000

    removed local_boxes stuff

Src/F_BaseLib/layout.f90

commit f69621cccc4432e57ca449f9d70a2683856fd0a3
Author: lijewski <lijewski>
Date:   Fri May 20 20:42:29 2005 +0000

    added multifab_internal_sync_c

Src/F_BaseLib/multifab.f90

commit 654d02f2f3daf07f7abbc92fc3fd21702e7b6707
Author: lijewski <lijewski>
Date:   Fri May 20 18:22:09 2005 +0000

    more copyassoc stuff

Src/F_BaseLib/layout.f90
Src/F_BaseLib/multifab.f90

commit 715ab5a1d2136a6e99c0e987051f261c724ac179
Author: lijewski <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 712c890599b75c03c399b40df661bc3eb087debb
Author: car <car>
Date:   Wed May 18 21:16:28 2005 +0000

    try to get the alpha term right

Src/LinearSolvers/F_MG/stencil.f90

commit 8d8cf1419283ebe6e5c5527c46d3b1df757357fb
Author: lijewski <lijewski>
Date:   Tue May 17 22:03:17 2005 +0000

    copy fixes

Src/F_BaseLib/multifab.f90

commit 505c83fc32011603b539ceffab36249d83a631a8
Author: lijewski <lijewski>
Date:   Tue May 17 22:02:53 2005 +0000

    added component to debug output

Src/F_BaseLib/fab.f90

commit 0c73e0b8a4c4bab40cb14afeaf22f508946afd3a
Author: car <car>
Date:   Tue May 17 20:46:41 2005 +0000

    false alarm

Src/F_BaseLib/fab.f90

commit 601c7a23874bfc4f75ad60b5068ccf3c58580f79
Author: car <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 845dbd1a2ce001b6404575573134c48b5fdc862f
Author: car <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 12628509b6f3cd547a59393aca3362a334d415b0
Author: car <car>
Date:   Tue May 10 22:11:41 2005 +0000

    print generic for ml_multifab

Src/F_BaseLib/ml_multifab.f90

commit b59b14683e5351d71774f0502e96999a775d84a3
Author: car <car>
Date:   Tue May 10 22:11:11 2005 +0000

    simple abec code

Src/LinearSolvers/F_MG/stencil.f90

commit 8c80088739a29dbdb5d8eb90baff071f641b49ef
Author: car <car>
Date:   Tue May 10 13:51:28 2005 +0000

    single component applicators

Src/LinearSolvers/F_MG/stencil.f90

commit 239ce091447c1ed4d1a5b60ec65b540588a11139
Author: car <car>
Date:   Fri May 6 19:59:11 2005 +0000

    select bottom level

Src/LinearSolvers/F_MG/mg.f90

commit bdc3397e953fc6186c9583165b5c1dcf1024c6ab
Author: car <car>
Date:   Thu May 5 22:32:58 2005 +0000

    more suger

Src/F_BaseLib/ml_multifab.f90
Src/F_BaseLib/multifab.f90

commit fa73ff57b108d37d3b61f2f97ac68719c1fff317
Author: car <car>
Date:   Thu May 5 22:32:47 2005 +0000

    more options to output plotfiles

Src/F_BaseLib/fabio.f90

commit b04476eef0be369dc574cc8446013758af20bd02
Author: car <car>
Date:   Thu May 5 22:32:14 2005 +0000

    not needed modules

Src/LinearSolvers/F_MG/ml_cc.f90

commit b6cc62cec353a1f397cb577948d4a3924be81b52
Author: car <car>
Date:   Thu May 5 20:29:11 2005 +0000

    PROF only uses BLMpi.cpp

Src/C_BaseLib/Make.package

commit 085d869eb2d0c468608660c67c182635988647c9
Author: car <car>
Date:   Thu May 5 04:35:01 2005 +0000

    more suger

Src/F_BaseLib/ml_multifab.f90

commit 7269347d2f545f96619d8e65acf9edf075d7e615
Author: car <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 3f9c22f4b5396a142c417f63ccff4a3e0d9c899f
Author: lijewski <lijewski>
Date:   Tue May 3 17:46:01 2005 +0000

    oops

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 2224e50c0b413a2cf4a31e1c178b4dfea6aeedda
Author: car <car>
Date:   Fri Apr 29 20:34:15 2005 +0000

    layout lev 1 owns finer level layouts

Src/F_BaseLib/ml_layout.f90

commit fe3101bd51670cbcdd4b8e653d345098cb57b937
Author: lijewski <lijewski>
Date:   Thu Apr 28 23:09:13 2005 +0000

    memory cleanup

Src/F_BaseLib/ml_layout.f90

commit 7a0d7b087f95295ade30388984bb33485d29bab8
Author: lijewski <lijewski>
Date:   Thu Apr 28 22:15:41 2005 +0000

    memory cleanup

Src/LinearSolvers/F_MG/ml_nd.f90

commit ffae07ae0a0f0d54dbdbdc1d62618c4b1cbfb734
Author: lijewski <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 b9cc765a043be4df9623028722d1a8b811bf35d6
Author: almgren <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 4d9352a3415b9865596e06445d8ae6a8154de25f
Author: almgren <almgren>
Date:   Thu Apr 28 16:54:04 2005 +0000

    Need this change to make nodal work.

Src/F_BaseLib/fabio.f90

commit 518b9b8cc9a9aec6f6413900683d838ad0378c47
Author: lijewski <lijewski>
Date:   Thu Apr 28 16:31:12 2005 +0000

    simplification of buildFPB()

Src/C_BaseLib/Geometry.cpp

commit f1eeb40d8594cd1d7842d7e57e2e783fde0a6938
Author: lijewski <lijewski>
Date:   Mon Apr 25 18:25:56 2005 +0000

    nodal fix to set_bc_nodal

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 60ac15e4b1cec652cda97ac98a436ecacb216147
Author: car <car>
Date:   Sat Apr 23 19:49:49 2005 +0000

    sparse data distribution speed up

Src/C_BaseLib/FabArray.H

commit ee07e3f054e0d70267cb7a5800c2908fa69fd8d2
Author: lijewski <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 f2d78dfe4c29a17009e26c1e0840094e8ea23d9f
Author: car <car>
Date:   Fri Apr 22 17:24:16 2005 +0000

    added profiler

Src/C_AMRLib/AmrLevel.cpp

commit 8dd6aa0529e4f3ab333d8a33318f5b013c78d7ae
Author: lijewski <lijewski>
Date:   Fri Apr 22 02:35:30 2005 +0000

    Array<int> -> Array<char> 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 70da6521c0da7695ec28299a18ea5d63549cb609
Author: lijewski <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 d57b6d2b53bdcba71f9a6b422bad31cef7188c4c
Author: lijewski <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 de69f187aff907e2dd85c06fd1b26bedff1a3174
Author: almgren <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 0bb03f62223efc12d5d33b231b82b9a2f8beb426
Author: almgren <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 64e1180097ddd92f7d5f7684f2d9693a2f2236d6
Author: almgren <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 edf02c7aa0af9912fddaeefe324974621a654b54
Author: almgren <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 d5628fb125b19bd0000375c7a32fa943b04c19ca
Author: almgren <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 96d1df6ec0d8f8b2304f5bbb7ca5d531b59b4468
Author: car <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 5bd69fb0e8b19d7799e7bdfedeb90830a251212a
Author: car <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 de542e2d4effacb9c477ad7152db8758cd739ecb
Author: car <car>
Date:   Tue Apr 19 03:32:37 2005 +0000

    hate assert

Src/F_BaseLib/bl_error.f90
Src/F_BaseLib/boxarray.f90

commit 72e0d1f75bc67ea758f6e18f6b0daf68a5aa3dfc
Author: lijewski <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 af7852e432f1f64387689ed5b35c4f44adc2f56d
Author: lijewski <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 0bf4a39511ace0c9ea88ad8a5be0d6444558e727
Author: car <car>
Date:   Mon Apr 18 16:25:57 2005 +0000

    ml_nd

Src/LinearSolvers/F_MG/GPackage.mak

commit a70dd034735009f32191aa6158070a56b658a65a
Author: almgren <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 6deb4f58af1b6ee2f83bf98fb700920f93107ede
Author: almgren <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 e5971e090e4c9d4d8c25442ebfad099ab82e1b2c
Author: almgren <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 b8b5522b61bcd039b556a9fc4308acbfb29c923d
Author: lijewski <lijewski>
Date:   Thu Apr 14 23:22:36 2005 +0000

    fixed typo

Src/F_BaseLib/multifab.f90

commit 059eaedfa80f8f95c98cec177bd65ec2a7385556
Author: lijewski <lijewski>
Date:   Thu Apr 14 21:50:11 2005 +0000

    Now pretty print nodal masks.

Src/LinearSolvers/F_MG/stencil.f90

commit fd685fed04259a0ee7e5f10739effdaa4df5f68e
Author: lijewski <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 dffd1d0f79389465365bae420e904e413f209925
Author: almgren <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 290209737e13f192290d7a9c0710f8459398fa12
Author: almgren <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 d444aeb9818da54e96df0e2581696e12aa3d6a16
Author: almgren <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 de18cd3255f6d27d4dd3194c4ae968358224eb5a
Author: lijewski <lijewski>
Date:   Wed Apr 13 15:59:26 2005 +0000

    fixed some typos

Src/F_BaseLib/parallel.f90

commit 8fdfa67b83958ae584a29dd86aa44c5ea764da43
Author: car <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 e9f7803fbc9b2b44f2ffa0ab7508b1426aeed1c0
Author: car <car>
Date:   Tue Apr 12 23:21:01 2005 +0000

    bcast error condition

Src/LinearSolvers/F_MG/mg.f90

commit 86a5a06b734fc26873c0821b4ac17fb1f2785da0
Author: car <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 dec55c0d8d84c70b8a7548f4d3ca45c316c91c74
Author: lijewski <lijewski>
Date:   Tue Apr 12 20:30:15 2005 +0000

    Added call destroy(mm_grown)

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 22c675dea9c5a1bcee14706723034209729099d0
Author: lijewski <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 c01ce75ca21f3ad2cf4800a923866c46aa3b9e7d
Author: almgren <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 6bb2a36fc9aced418fc814bf3754168df7b51c5f
Author: lijewski <lijewski>
Date:   Mon Apr 11 17:57:26 2005 +0000

    Fixed bug in copy() routines.

Src/F_BaseLib/multifab.f90

commit 00e7fa3fa3970175e418c9c1b943a723cab871f2
Author: car <car>
Date:   Mon Apr 11 17:33:07 2005 +0000

    parallel

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 0c7608df8c18edba3963d0a47c5f260455be3943
Author: car <car>
Date:   Mon Apr 11 16:31:47 2005 +0000

    reclaim memory

Src/LinearSolvers/F_MG/mg.f90

commit 03d9ebda05e573cc35922d96338746d57955e446
Author: car <car>
Date:   Sun Apr 10 00:50:14 2005 +0000

    fix up that bottom solver...

Src/LinearSolvers/F_MG/mg.f90

commit 10e643ff26993b2c4b4102abcd799bdd10590e2d
Author: lijewski <lijewski>
Date:   Thu Apr 7 22:51:31 2005 +0000

    -O4 buggy on AIX

Tools/F_mk/GMakedefs.mak

commit 9d3df7efb8cc39d13909ed95654cab9c8f48c877
Author: lijewski <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 61fd8f7bb99e268a0b56738b31a8832ff39cb4b9
Author: car <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 afc844ce9f47ff0f5e8a92d9c55180299fb1d655
Author: lijewski <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 fb1c69eba5de3a114bef6a09662d0ca41a911a88
Author: almgren <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 e48625c76e93dc011f88fbdf3497f3b5250a83e5
Author: car <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 c478355cb44d554451771036e1445567fc4a56bc
Author: car <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 7f2bc428b0c22f02771c7474bbc30b99c2b1d31b
Author: car <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/mboxarray.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 30d24161f084eb36287d2a1e2ec8fa7bab8ce56a
Author: welcome <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 f46cb0467abc7ff5fc62459910a59c56ab7a456c
Author: lijewski <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 2549f66d12bddc021a77a31df59b38c2197ce002
Author: lijewski <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 431aef71b54a1bf666969c5fd5ae506de0c19cfc
Author: car <car>
Date:   Tue Mar 22 22:59:07 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/mg.f90

commit 30b44913d257d9975dbb10fe2522781f51f4e36d
Author: lijewski <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 5fa4d71f44f1abc0b29e8cde200f036e864feca4
Author: lijewski <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 e33db700f956accb727755d58f1a7dda1438fd73
Author: lijewski <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 6284cf110b8e2b8da04c7cdcf38382aea3731d28
Author: lijewski <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 c855c190cec7a9ba95df8496081d743893c4dfee
Author: lijewski <lijewski>
Date:   Tue Mar 22 19:23:08 2005 +0000

    Progress merging in periodic stuff.

Src/LinearSolvers/F_MG/stencil.f90

commit 59d35142c206e9a3a886e35e79ee535871ad4f97
Author: car <car>
Date:   Thu Mar 17 23:34:52 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit a9eb87f03f6583beefc67862d10299dd2347f061
Author: lijewski <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 50c617983f30fe6eb9da9e66fbe4561a166303e6
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:57:25 2005 +0000

    slight code rearrangment

Src/F_BaseLib/boxarray.f90

commit 63d189941796cdf39c425db3f70dee322dd9e6ae
Author: lijewski <lijewski>
Date:   Thu Mar 17 21:56:54 2005 +0000

    Added optional cross argument to fill_boundary.

Src/F_BaseLib/multifab.f90

commit 7c6a8ef5b97aedd146c6b81e26b11c7feea1001e
Author: car <car>
Date:   Wed Mar 16 23:33:59 2005 +0000

    corner/edge extrap

Src/LinearSolvers/F_MG/stencil.f90

commit e0a5c1ba7a6361330e9197f3937d95f049779132
Author: lijewski <lijewski>
Date:   Wed Mar 16 21:56:00 2005 +0000

    Added boxarray_box_corners()

Src/F_BaseLib/boxarray.f90

commit 8fbafa6ad02ae7d0f5b74db554c488db974e8ac0
Author: car <car>
Date:   Wed Mar 16 19:00:42 2005 +0000

    OMP syntax fixes

Src/F_BaseLib/multifab.f90

commit c382b7dad97d5d93cfdaebb69a86429e9ebe74ca
Author: car <car>
Date:   Wed Mar 16 17:30:23 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit d015d860820ec5b6eb372747ed98ce9cca6d2adc
Author: lijewski <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 7d07d35b542792d5999b4a51d587d156a17a8dcd
Author: lijewski <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 8bc9e888620bc9863cbf70f5245348bb86dd7550
Author: lijewski <lijewski>
Date:   Tue Mar 15 20:59:38 2005 +0000

    slight change in notation

Src/F_BaseLib/box.f90

commit 347af29371a229892b5b99ba22644c7e0f837b00
Author: car <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 7f81cd25274dd2eb189d582996b2915a4d09e6a6
Author: car <car>
Date:   Mon Mar 14 22:56:37 2005 +0000

    denodalize

Src/F_BaseLib/box.f90

commit d82cd85c187342f544e07e27ef090e70c596152b
Author: almgren <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 b78b3d3d021a100f42ca822e185f4f8cf126b85c
Author: car <car>
Date:   Mon Mar 14 20:45:11 2005 +0000

    add flux_reg.f90

Src/F_BaseLib/GPackage.mak

commit ea66d591c989c57b49dac9a8b3c8884503e379f4
Author: car <car>
Date:   Mon Mar 14 20:44:50 2005 +0000

    read nodal mf

Src/F_BaseLib/box.f90
Src/F_BaseLib/fabio.f90

commit 3a5230cdb54eeaaa25ba51a5f43732e7cf0e91b6
Author: almgren <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 d1479ef5168ded053be25fd0916ce760a878ea00
Author: car <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 44120521c83f23091ed5a58bb47695094aeeb285
Author: car <car>
Date:   Sat Mar 12 14:39:49 2005 +0000

    mac i/o is like aix

Src/F_BaseLib/fabio_c.c

commit 746f066a7a7fe26a7a7345ae802a8a33792a4309
Author: lijewski <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 8f0340d43ba867df05f9d111a4d88739e32821d9
Author: lijewski <lijewski>
Date:   Sat Mar 12 00:23:34 2005 +0000

    A little simplification.

Src/F_BaseLib/layout.f90

commit 924d07072ac7aad52ab20911f784a0cf2f996078
Author: lijewski <lijewski>
Date:   Sat Mar 12 00:22:31 2005 +0000

    periodic_shift() -> box_periodic_shift()

Src/F_BaseLib/box.f90

commit 7afce3f74b647b2b3edde7f7b360145e6bd19491
Author: lijewski <lijewski>
Date:   Fri Mar 11 22:28:16 2005 +0000

    Added box_contains_strict()

Src/F_BaseLib/box.f90

commit facbf2546309ab6a5ba09efa3ff60d5f915c9784
Author: lijewski <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 5e58d7012de230336cdd7225f1fe3bea34165e46
Author: lijewski <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 64610e073a663da624aa8ee0908b4cd28d894255
Author: lijewski <lijewski>
Date:   Tue Mar 8 21:50:44 2005 +0000

    Some progress on making fill_boundary periodic-aware.

Src/F_BaseLib/layout.f90

commit 5f98228a49bf7ede464547465d347892e098619d
Author: almgren <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 3cd413d31764582e6437603defcf31e60ded960f
Author: lijewski <lijewski>
Date:   Mon Mar 7 23:11:41 2005 +0000

    Looking good.

Src/F_BaseLib/box.f90

commit 9d03035567a6e9cd50e628bdd1874c171d3d7954
Author: almgren <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 e0da2122c4da8727499536e990a3967ea78a8db5
Author: lijewski <lijewski>
Date:   Mon Mar 7 21:52:39 2005 +0000

    Rewrote a few things slightly differently.

Src/F_BaseLib/box.f90

commit 0d2d9ad326cd466a442a0b48bf2367730bc4a7f5
Author: almgren <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 63737243dde922fc7449ffa8f7595555e8d78073
Author: almgren <almgren>
Date:   Mon Mar 7 20:28:56 2005 +0000

    Fixed Neumann bug in 2-d.

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 6ec012c27ef055f4b0311eb7ef8f09a4d4f38e84
Author: almgren <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 ec5b6130ec773b1f208b9cf2b3ecd06ecf63c7c2
Author: car <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 a6b69e4612a7a7d153ac33d3067ffb3c5d83eec1
Author: car <car>
Date:   Fri Mar 4 20:25:48 2005 +0000

    remove extraneous print statments

Src/LinearSolvers/F_MG/stencil.f90

commit 643db54ba72e4577925314af1984dd0dbffd51bc
Author: lijewski <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 ff4a0e251f1998d1990b5a55ad74d2d3d4ea6271
Author: almgren <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 7acfa510f0fac5ab69b6ca0110c030603dca1eb5
Author: car <car>
Date:   Thu Mar 3 02:25:05 2005 +0000

    -C converts cvmgt to MERGE; as per f90

Tools/C_scripts/strip72

commit 75ca1c28ed9e6641a4a5ffec9df8b288029a3653
Author: almgren <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 f9c6212d59473788a97b03b6dd616b24ea03c2e4
Author: almgren <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 8362b21c01da3769f4ffa0bb8ef552a978ad07be
Author: almgren <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 497ddc4db2750aab85118d43290fb9277473b2c0
Author: almgren <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 4281fd2d96ace885d8449ad0412e7ee0e9f843e7
Author: car <car>
Date:   Wed Mar 2 17:42:56 2005 +0000

    newest intel 8.1 fixes check shape pointer

Tools/F_mk/GMakedefs.mak

commit a204d43275606ecfeaa766b84328f5467ff30ede
Author: almgren <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 db778753f68d7e99a01bce1e1ed9777a15a13c7d
Author: almgren <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 c9248a50393df1c4e8854176028170dae54ec18f
Author: almgren <almgren>
Date:   Tue Mar 1 20:03:25 2005 +0000

    Clean-up...

Src/LinearSolvers/F_MG/sparse_solve.f90

commit 1bb5d5437dae70a59025981e0be280b97fb2aafb
Author: car <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 fb893953604dc54a038454f54307c447844eb9cf
Author: car <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 7577f4214fd6e1054cd3a790986e220521f6ef34
Author: car <car>
Date:   Sun Feb 20 16:50:57 2005 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 8edcef40a24e07ee9a6c58cd65f4f15ac3dd5478
Author: car <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 7fff51f57a925beb0ba18322fbe02f6a5d60ee65
Author: car <car>
Date:   Thu Feb 17 23:21:09 2005 +0000

    debug and opt flags for IBM on Mac

Tools/F_mk/GMakedefs.mak

commit 223576640b62ab5f1d8e7e207539a809d990a93b
Author: car <car>
Date:   Thu Feb 17 22:03:31 2005 +0000

    no stinking mutex's

Src/C_AMRLib/AmrLevel.cpp

commit 78fcf3e4826886bace690d4c6d7bf77b944387b1
Author: car <car>
Date:   Wed Feb 16 23:10:40 2005 +0000

    more arithmetic in multifab

Src/F_BaseLib/multifab.f90

commit 2dc1d5251a33ff9dbefe7d9d7ba211739f5ba731
Author: car <car>
Date:   Tue Feb 15 21:54:19 2005 +0000

    more dft debug changes

Src/F_BaseLib/multifab.f90

commit 77f35293566112fa0740bedf329889e03d9138cd
Author: car <car>
Date:   Sat Feb 12 20:15:43 2005 +0000

    MPI_recv takes a status argument

Src/F_BaseLib/pingpong.f90

commit 3e6f7ed20ce52e0bb7ea4732f2bf382436d0dbf7
Author: car <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 54650db2c54a9806499960767079f3558682f9a9
Author: car <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 cb85f37df84c099a99833faa6b27de9e468f2155
Author: car <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 7466be6c3d5ba96622264b4a8d72b735dade700d
Author: lijewski <lijewski>
Date:   Wed Jan 26 23:20:51 2005 +0000

    Got rid of std::pow() call.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 0ef3e14a42bf16c1c8c82b5caedfb0a33fb532d5
Author: lijewski <lijewski>
Date:   Wed Jan 26 23:20:30 2005 +0000

    Got rid of std::pow().

Src/C_BoundaryLib/InterpBndryData.cpp

commit 2b0085a76d76a4461504789a4f3807755d799a2b
Author: lijewski <lijewski>
Date:   Wed Jan 26 22:52:54 2005 +0000

    Fix for Jacquard.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 4694b7376b40e4af2981ce264d977ad19383160b
Author: car <car>
Date:   Wed Jan 26 16:33:15 2005 +0000

    fancy gfortran

Tools/C_mk/Make.defs

commit 1886c91b2b00a4ca3bbee7527d7a2bc39b9abf8c
Author: car <car>
Date:   Wed Jan 26 16:31:27 2005 +0000

    fancy gfortran

Tools/C_mk/Make.defs

commit 31af8966f0588b7c0c4e8e595f4172a7bc9a3692
Author: car <car>
Date:   Wed Jan 26 00:20:31 2005 +0000

    crafty way of getting path to libf95.a

Tools/C_mk/Make.defs

commit 9a6a458e7d026de6650ddcf8ff29b5d4330da476
Author: lijewski <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 b2b8b12138bbcb4ab0e9438345cb629915f2d982
Author: lijewski <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 52df063b8527b250cbb76b99ad1cf1389dce8a2f
Author: car <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 a7b134be839c399a3e2675f93cf224eda45f10fe
Author: almgren <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 0ff436a8493e00a59a66ffba75a446135aa322f0
Author: car <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 d87e8956480f87356fa944e67fcf3cfbed22a790
Author: lijewski <lijewski>
Date:   Fri Jan 7 17:38:55 2005 +0000

    fix to operator=

Src/C_BoundaryLib/BndryRegister.cpp

commit ba43c235da5d003c18bdc7e0f8dcddd73d2f9112
Author: lijewski <lijewski>
Date:   Thu Jan 6 22:18:50 2005 +0000

    extra gunk for LAM

Tools/C_mk/Make.mpi

commit dd4300d1e0e80fbc607ab8e1086cb8615ea4edea
Author: lijewski <lijewski>
Date:   Wed Jan 5 22:19:46 2005 +0000

    fix to operator=

Src/C_BoundaryLib/BndryData.cpp
Src/C_BoundaryLib/BndryRegister.cpp

commit d373c725ebfde4f08178062fe480b22de8c4cb29
Author: lijewski <lijewski>
Date:   Wed Jan 5 21:53:21 2005 +0000

    fix to operator=

Src/C_BaseLib/Tuple.H

commit 80a757a63aac918a136c8d4e31783714b2bfa567
Author: car <car>
Date:   Tue Jan 4 23:33:22 2005 +0000

    JEFF_TEST turns on mpi_waitall

Src/C_BaseLib/ParallelDescriptor.cpp

commit 0ce815802066bd6a84dec411d54d94d1d27246de
Author: car <car>
Date:   Tue Jan 4 22:36:15 2005 +0000

    name map

Tools/C_mk/Make.frank

commit 41f3ce57f65e219df6a8c838ffec2f3103089866
Author: car <car>
Date:   Tue Jan 4 22:10:41 2005 +0000

    frank archive file

Tools/C_mk/Make.frank

commit 3056e90423b8113e74ddde99d0eacfc82b0dccf4
Author: car <car>
Date:   Tue Dec 21 17:10:59 2004 +0000

    g95 tweaks

Src/F_BaseLib/filler.f90
Tools/F_mk/GMakedefs.mak

commit 945f35161bae04c071b2ac8b1e4d83140d804773
Author: car <car>
Date:   Tue Dec 21 15:32:03 2004 +0000

    darwin

Src/F_BaseLib/GPackage.mak

commit 6f648d485d3bee84095fa75b6c3ea165ae999cda
Author: car <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 e693758a45bdab651d08ac546e66f161d97bdf68
Author: car <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 83e65108d6ffaa8c6976cd45d7f194376486191d
Author: car <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 d91e017a0c3d15a8e984aa1a3a497d48b510a50a
Author: vince <vince>
Date:   Thu Dec 16 20:36:54 2004 +0000

    this version works for me using CC.

Tools/C_mk/Make.IRIX64

commit 1171421c30bafb5738a14910f3336ab81293fc8c
Author: car <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 232f3686b8f6f8163e747b760a90bdcc74ade7fe
Author: car <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 c0a0bc853310e03993b55900d76745cd1dbf97b7
Author: car <car>
Date:   Wed Dec 15 18:06:54 2004 +0000

    stupid warning wrap w/ IOProcessor()

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 6829cbaffba77ebd4d9b8aacc40ceb505341656e
Author: lijewski <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 eb22be597d93b8e1ab962be51491bdcffae05d39
Author: car <car>
Date:   Fri Dec 3 18:54:52 2004 +0000

    clean/realclean not as painful

Tools/C_mk/Make.rules

commit eeba26b049c5062575ff49c37b14bba8d10f5ad7
Author: car <car>
Date:   Fri Dec 3 17:44:04 2004 +0000

    *** empty log message ***

Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak

commit d0d14639316f7e02ca18358858595bd6d3ab3d42
Author: almgren <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 698757470244c1323ecfe9575926d19633144132
Author: lijewski <lijewski>
Date:   Tue Nov 30 19:21:09 2004 +0000

    added Compare class

Src/C_BaseLib/IntVect.H

commit e3085ac168606d5f87e8633faf1d5535a97f4f64
Author: almgren <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 3991c95a3899a00b4bfa745d7f93b75f33c9b77e
Author: almgren <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 9eaf9909e5164f76ffb2331aaaf0d07f1deab45a
Author: almgren <almgren>
Date:   Mon Nov 29 22:40:30 2004 +0000

    Removed print statements.

Src/LinearSolvers/F_MG/mg_smoother.f90

commit 0453e2a5dd7e98454154b88a8500b26b9d911661
Author: car <car>
Date:   Mon Nov 29 20:53:24 2004 +0000

    bc interp renewed

Src/F_BaseLib/GPackage.mak

commit a6bbf95cff76072abe1159ea9b937d631fcdbec7
Author: almgren <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 a4db5825943beb3e0c42baec181ef51c16541af5
Author: car <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 732f381f49c7a13e78d5d67d8e52b27fbfb20feb
Author: almgren <almgren>
Date:   Fri Nov 19 20:28:22 2004 +0000

    Bug in index loop for defining voffx.

Src/F_BaseLib/interp.f90

commit ec14c86bf388cca65d544c57f2cf44556418302b
Author: car <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 9811cec7bfdfe326b38ddf7d55b657e3aca57e4b
Author: car <car>
Date:   Thu Nov 18 17:42:01 2004 +0000

    XLC fixes

Src/F_BaseLib/multifab.f90
Tools/F_mk/GMakedefs.mak

commit fb07e869a2f98934edfbd9ee82ead4fad56a9b61
Author: almgren <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 10b59b398742b7ef82602ed430cbda930c6e35ad
Author: car <car>
Date:   Wed Nov 17 20:08:25 2004 +0000

    using lbound,ubound should work

Src/F_BaseLib/multifab.f90

commit 6c288d3720622d32e4a3c0c8704a68f007a62801
Author: car <car>
Date:   Wed Nov 17 19:09:22 2004 +0000

    multifab_fab_copy

Src/F_BaseLib/multifab.f90

commit 5e5813233225f3972f1aade0d2fe8f86114532d7
Author: car <car>
Date:   Wed Nov 17 16:29:36 2004 +0000

    FreeBSD

Tools/F_mk/GMakedefs.mak

commit f1a903a5c8d37a60405e85bc5ddef7afac822759
Author: car <car>
Date:   Tue Nov 16 23:56:24 2004 +0000

    order of include Darwin?

Src/F_BaseLib/timer_c.c

commit 316c6675e78db7903fe7f4d36fb7e85c29b87fcf
Author: car <car>
Date:   Tue Nov 16 23:21:19 2004 +0000

    MacOS X

Src/C_BaseLib/FPC.cpp
Tools/C_mk/Make.Darwin

commit f5fea6f5db341cad89d17fe27c43777bd60903ce
Author: car <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 5f5ae259a5827657a460babaa28fdaf547da91ba
Author: car <car>
Date:   Fri Nov 12 20:55:33 2004 +0000

    gotta go home

Src/LinearSolvers/F_MG/stencil.f90

commit b746b42a3428baa38e3864238f9e3936b792704a
Author: car <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 5edf0ed64e25afd7f298396ef19acf1888ac05c0
Author: car <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 39c5d7f49cd42bf4476638508ce1a6993303df30
Author: car <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 5ea8c2b4f571f5a3d4d7adb6381396816118baac
Author: car <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 38376488dbd1f0ce201d9554e5829fd9d3993ad1
Author: car <car>
Date:   Fri Nov 5 19:11:16 2004 +0000

    MLW: barrier in glean prevents buffer overrrun

Src/C_BaseLib/BLProfiler.cpp

commit 6b13143dc89d537b7cfbb3644776962e0ad005a8
Author: car <car>
Date:   Thu Oct 28 19:17:15 2004 +0000

    tweak

Tools/F_mk/GMakedefs.mak

commit b59f423a4e337ad097760bbb10cfbc099ffb387b
Author: car <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 71e542453f0335ca124d5dc65376dbc92849f6dc
Author: car <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 cf6a5d03406c1f624bfbe8b26aa35b4911e5db97
Author: car <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 d6108e7e002f8771f9afc37023c3b00a44d41409
Author: car <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 c89e9175809c9167744d9a822ce90a50f3060b9e
Author: lijewski <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 bde5769088e68fda4a56b1b96c211b427acb2abc
Author: lijewski <lijewski>
Date:   Wed Oct 13 20:57:03 2004 +0000

    output a bit more stuff

Src/C_BaseLib/DistributionMapping.cpp

commit 59f5d7867122d506f8689399c9c45d045cdeaad2
Author: car <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 ef0afc70ebdf783397110feea8ee7f51b0f6c067
Author: car <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 8cc383b24a19da81507a4baabe5d3495fe68a70b
Author: lijewski <lijewski>
Date:   Mon Oct 11 22:45:37 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit a2147c43f35e4a9db339db6d4ca2e11a7c2201f9
Author: lijewski <lijewski>
Date:   Mon Oct 11 22:00:12 2004 +0000

    Fixed Chuck's bug

Src/C_BaseLib/DistributionMapping.cpp

commit c7007acb6a3b385e7f0a9b2be20afb0bdfec781a
Author: lijewski <lijewski>
Date:   Mon Oct 11 21:57:09 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit 05ac385569218889d221395c31d87e28aface89b
Author: lijewski <lijewski>
Date:   Mon Oct 11 21:47:03 2004 +0000

    *** empty log message ***

Src/C_BaseLib/DistributionMapping.cpp

commit c01ae1f75894a8e8cc3ca61aa1884952e07bbf71
Author: car <car>
Date:   Mon Oct 11 21:17:13 2004 +0000

    for metis

Tools/C_mk/Make.defs

commit 7c6af15f41bbd82c173242d01cfc4e8ba8ebe5d2
Author: car <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 f1b7d50f6738532d13e8ee101e79c52333bc5fc0
Author: car <car>
Date:   Mon Oct 11 20:20:47 2004 +0000

    added metis

Src/C_BaseLib/DistributionMapping.H
Src/C_BaseLib/DistributionMapping.cpp

commit 962a074b1930f38dc1315a6e2d4c10158b62164e
Author: vince <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 db5b010056afc06266c620da29fd00226a1e14f8
Author: car <car>
Date:   Tue Oct 5 01:41:46 2004 +0000

    minor fixes

Src/F_BaseLib/fabio_c.c

commit c5939d3e5e635000f51e8e54a8fcb7950e6c579c
Author: car <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 a79560c415793171bf9ab8efa91a2b17c154b292
Author: car <car>
Date:   Mon Oct 4 19:41:54 2004 +0000

    ml changes

Src/F_BaseLib/multifab.f90

commit 5d9dc9e2fcb206bf501f157952142d4d46e31393
Author: car <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 4373c344a33b2d134c32e5e566de5fbeb17db016
Author: car <car>
Date:   Thu Sep 30 19:02:41 2004 +0000

    corrected fab dimensions

Src/F_BaseLib/fabio.f90

commit 5015be84b9445ca2af35023ac0989a1d74661175
Author: car <car>
Date:   Tue Sep 28 17:56:35 2004 +0000

    formatted io for plotfiles

Src/F_BaseLib/fabio.f90

commit 52e52ac63ea9d3e1c2730c22c0dce956a50f8fb5
Author: car <car>
Date:   Wed Sep 22 17:53:41 2004 +0000

    more constants

Src/F_BaseLib/bl_constants.f90

commit 79f4dec7a53485da670fca9994461c115824e1a9
Author: car <car>
Date:   Tue Sep 21 17:38:17 2004 +0000

    fixes for ia64

Src/F_BaseLib/mt19937ar.f90

commit cbb241d709212f9dc94dc19db954f05755c2c7e5
Author: car <car>
Date:   Mon Sep 20 21:49:34 2004 +0000

    make extrap bc eat boundary value

Src/LinearSolvers/F_MG/stencil.f90

commit 87a1fa5e65f6e852d4bd4551b738aeb15f925911
Author: car <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 5f2cf673bab8fcb9bf233166e1bd1d628917a56c
Author: car <car>
Date:   Fri Sep 17 20:30:36 2004 +0000

    Make.IRIX64

Tools/C_mk/Make.IRIX64

commit 26d496ec631acd25b6eff18b4a2d4691b7f4b9c8
Author: car <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 9762316222b4e634c71ae3232e994f30a39f25b2
Author: car <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 0ddeb1aeae75f1c7b16424535c3266bfd2a3b3cb
Author: car <car>
Date:   Mon Sep 13 19:55:34 2004 +0000

    *** empty log message ***

Src/F_BaseLib/f2kcli_crayx1.f90

commit 67ab67e1bb2f57d2dc17dfda7cbe7823a7032de2
Author: vince <vince>
Date:   Mon Sep 13 19:02:23 2004 +0000

    flags for cxx.

Tools/C_mk/Make.OSF1

commit 23a9eeec7f700aa4a6cdf0a39771ffbd5efec269
Author: car <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 c1dc0557dcbcf63d9f02764c88db1d30e9a232c9
Author: car <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 a8218a6fc0d4a8f45eacf7d8c1e27c72525a5884
Author: vince <vince>
Date:   Fri Sep 3 23:59:19 2004 +0000

    added check for capfinestlevel.

Src/C_AMRLib/StationData.cpp

commit b80413555b22bf2570226bc24d4596d3ad1b7bc0
Author: welcome <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 e6f95a0f1464dc26551f6b567062dfe3a54e0b24
Author: car <car>
Date:   Wed Aug 25 19:32:27 2004 +0000

    FCOMP=g77

Tools/C_mk/Make.defs

commit 77e3d3f9be567375b6bdfbe5a2d78b8893caee51
Author: car <car>
Date:   Tue Aug 24 22:33:16 2004 +0000

    Intel/Lahey fix

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit e724fd8e98d5df9ea42ecc341bfeb47f68933fd7
Author: marc <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 d49870db16594ffaaec9011ab8741f575a3b9913
Author: car <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 7495cfe27fbac5933b9d0bf68722a93a120601f5
Author: car <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 4603f3057f21cd04bb09188190b0b292ec654fb8
Author: car <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 beb03c69a5d2880111ec3c80e8d9cef4c5149f15
Author: car <car>
Date:   Wed Aug 4 19:53:26 2004 +0000

    more mboxarray stuff

Src/F_BaseLib/mboxarray.f90

commit 5c98f8e4903d5476b2625f57a2265de860a3d1fc
Author: car <car>
Date:   Wed Aug 4 00:52:04 2004 +0000

    windows update

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 88e7d21b2ad008090cace5fee834ca8a8d5f4ced
Author: car <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 64c7fbc68d16979f09288a7be375737d75e0da14
Author: car <car>
Date:   Mon Aug 2 22:11:38 2004 +0000

    *** empty log message ***

Src/LinearSolvers/F_MG/stencil.f90

commit 022ad48784ea49cd2db7498bb7c129f24e25847e
Author: car <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 4eef4aeeb736f685561989965fd5654e9abdd8fc
Author: car <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 3f27bdf455485d13eb19634a0efcef334fdcb678
Author: car <car>
Date:   Thu Jul 29 20:32:23 2004 +0000

    altrix

Tools/C_mk/Make.defs

commit c04d52dab2fe46440104468f5e99dc2773cfde47
Author: car <car>
Date:   Thu Jul 29 18:53:12 2004 +0000

    altix

Src/C_BaseLib/FPC.cpp

commit 442726a9614a3ad6c48f15cf7a308d5cff0b7f7c
Author: car <car>
Date:   Thu Jul 29 15:35:03 2004 +0000

    crayx1

Tools/C_mk/Make.CRAYX1

commit 4f555c329e2dc41ea3684b54b73e15eddba53d68
Author: welcome <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 f84dbf86452e727cdbe861fb8ae26f5c2b4ac35e
Author: welcome <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 80fdd17621677eeec7909651cd14c711171f3efd
Author: welcome <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 8710d2bc54febf3f7bc4493d7c3b5647d5d34fc2
Author: car <car>
Date:   Wed Jul 28 18:06:05 2004 +0000

    fixes for X1

Tools/C_mk/Make.CRAYX1

commit 65e55237e971c6e1b3eac5610ee6d9ea6fa7cf15
Author: vince <vince>
Date:   Tue Jul 27 22:51:25 2004 +0000

    added std::

Src/C_AMRLib/DatasetClient.cpp

commit 96d012f269fd1b69dda8642f4d39ec3460b22310
Author: vince <vince>
Date:   Mon Jul 26 22:24:29 2004 +0000

    call fix for arrayview.

Src/C_AMRLib/DatasetClient.cpp

commit 6b8b6a101c04688d26e5a057dba307754a8a8c4f
Author: car <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 446b995f0adcc43ac003959e8d741bc9df1f2b40
Author: car <car>
Date:   Mon Jul 26 20:49:09 2004 +0000

    gfortran trial

Tools/F_mk/GMakedefs.mak

commit 9f15aa3de73bca64c1ff4d578da9de1c18d15bbc
Author: car <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 70f528b3a225b78e47361144d6ce48fd3d88128a
Author: car <car>
Date:   Mon Jul 26 19:37:21 2004 +0000

    ihi->ilo

Src/F_BaseLib/interp.f90

commit 7d277ee899088f80007ff44381da042a84db603f
Author: car <car>
Date:   Mon Jul 26 19:36:59 2004 +0000

    pointer association, not

Src/F_BaseLib/cluster.f90

commit 4a70d1e85b0e15670f7f3eabf5eb2d7205868d52
Author: car <car>
Date:   Mon Jul 26 19:25:57 2004 +0000

    broken unitialized variables on IRIX

Tools/F_mk/GMakedefs.mak

commit 8d5942de36aba6db1cfe709e57e36a6a7154cf8b
Author: car <car>
Date:   Fri Jul 23 23:37:28 2004 +0000

    cray bug work around

Src/F_BaseLib/boxarray.f90

commit a290b2b64576fc2e44c961fdf2c14d9c8be43d41
Author: car <car>
Date:   Fri Jul 23 22:04:22 2004 +0000

    crayx1

Src/F_BaseLib/f2kcli_crayx1.f90
Tools/F_mk/GMakedefs.mak

commit 61148a6817bda09a95d284e1a036d0eb5f9603dc
Author: car <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 f824ce6082984ae8698e88bd51d06b041fd7da7f
Author: car <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 9d8ebb2112ca656edb544ef38a97cf0d05c50812
Author: car <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 6fa7455c4c41aecd67da4852ce53e8012ab20862
Author: marc <marc>
Date:   Thu Jul 15 17:16:50 2004 +0000

    Add BL_NOLINEVALUES to list of defines

Tools/C_scripts/dsp.mak

commit f60744ce1a945c7dea38a1d8ec2d90e507d573f7
Author: car <car>
Date:   Fri Jul 2 19:59:25 2004 +0000

    new types definitions

Src/F_BaseLib/bl_types.f90

commit 0de502bb2893474f5d056c87330e76d5bae34b63
Author: car <car>
Date:   Wed Jun 30 22:10:48 2004 +0000

    testing purposes

Src/F_BaseLib/bl_types.f90
Src/F_BaseLib/multifab.f90

commit 9b04d71a56755cf3f29df36e0226c7aee4ae0580
Author: almgren <almgren>
Date:   Tue Jun 29 20:19:45 2004 +0000

    Removed some print statements.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit 79506fb6bcb2e0acda0f9c33daab32a8f092a057
Author: almgren <almgren>
Date:   Tue Jun 29 19:58:48 2004 +0000

    Removed print statements.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit dcdceecd14df0b1c0e4d3561ae4a78df5cad8c4c
Author: car <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 6c0ad5b1d8b169ddb052777a479d169aadb08f3f
Author: car <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 8e41fe7ac969317c011e9a26722e37f1f3a5c15a
Author: almgren <almgren>
Date:   Fri Jun 25 22:38:30 2004 +0000

    Typo: had ny instead of nx.

Src/LinearSolvers/F_MG/stencil_nodal.f90

commit acdbf6089214f2f5a09cc546f973861d1d6d58a0
Author: almgren <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 ac44dd382d49fb9c634e5f1d5ee49d137543c3d7
Author: almgren <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 df6b9ad6b1cb988ce025fa0af4e94b4ffa16f6d4
Author: almgren <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 fbf4f926ab1b605006b87d0e6b2136d4112d818d
Author: almgren <almgren>
Date:   Thu Jun 24 20:22:32 2004 +0000

    Typo mis-spelling corrected.

Src/LinearSolvers/F_MG/stencil.f90

commit e38dfe967994adc89a395c9e3523645bf47f0e1e
Author: car <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 23c6934f1e448841fa53d0f68a5fc8b887a0affa
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco_e.FF
Tools/F_scripts/coco/coco_e.II
Tools/F_scripts/coco/e1.FF
Tools/F_scripts/coco/e1.II

commit d573fc321d34f6d3c3ade270cc1f2ee2f296765a
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco_e.II

commit acf74a2c568b193072d3c9162aceb5c794e89dbc
Author: car <car>
Date:   Tue Jun 22 16:42:05 2004 +0000

    *** empty log message ***

Tools/F_scripts/coco/coco.pl

commit 628bfa177914e36883cd27ff29ae8e0d8b7ba745
Author: car <car>
Date:   Tue Jun 22 15:11:43 2004 +0000

    initial

Tools/F_scripts/coco/coco.pl

commit c53adb7c0a46e77c401f003adc5d0e24bd3de5f5
Author: almgren <almgren>
Date:   Fri Jun 18 17:18:18 2004 +0000

    Need to check _comp instead of COMP

Tools/F_mk/GMakedefs.mak

commit bcaf2800c38029072295add0f1a90655577ee31e
Author: lijewski <lijewski>
Date:   Tue Jun 15 19:24:16 2004 +0000

    Added -mp flag

Tools/C_mk/Make.defs

commit 7929dbe96aa16ee9e25e765430eb5fbec688dc19
Author: car <car>
Date:   Fri Jun 11 21:42:21 2004 +0000

    *** empty log message ***

Src/F_BaseLib/bl_timer.f90

commit 7ae0215084b7607aabbaf69510516d02bd95abda
Author: car <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 65d9574f6f012c4351ef51898225ed7172163616
Author: car <car>
Date:   Tue Jun 8 18:14:34 2004 +0000

    *** empty log message ***

Tools/F_mk/GMakerules.mak

commit f59d86e7c3c51f36450a16c733c771add521f5bf
Author: car <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 1c9ae8a21ce967aa40058d08c09c4ab75169eeb6
Author: car <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/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/knapsack.out
Tests/F_BaseLib/t_knapsack.f90

commit 363cae8822785d89f3248568bf3b3078352b561d
Author: car <car>
Date:   Mon Jun 7 15:56:59 2004 +0000

    formatted output

Src/F_BaseLib/test/knapsack.out
Tests/F_BaseLib/knapsack.out

commit 6501fe356392b4b9c5230d4572487d5c7ed84f9c
Author: car <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 37a7bddfcf3ae9f34b7abf1f4331f9bca0f1cf4c
Author: car <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 14fd6638f790424d31790a16d61877261908d21d
Author: car <car>
Date:   Sat Jun 5 15:07:18 2004 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Tools/F_mk/GMakedefs.mak

commit a553dc438b106269fb89df6c088a282ba8a4cc0c
Author: car <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 040b644d2917423108971883f11649e72f786c16
Author: car <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 172a734048cd6a21c6b58e73608e455d0f39bdf3
Author: car <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 e1a9316f5d8575f59208c51fb344dba8aa4e81de
Author: car <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 bbcbdafcff3365d2aa2be028a4821de07778b779
Author: car <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 aa7128751bdc66db2756c2474d632656b70f74e0
Author: car <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 443aeceb41b4691c6250b1cda85af7cd1e89b396
Author: car <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 c7ebd079b02a683f0584aec5672c119ecf144ddb
Author: car <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 89329559317c76be46eeb1086800988bb08afbd0
Author: car <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 8dbbb0e9279b940a35b2880df43370858eeadbb4
Author: car <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 704ff60a87090371e438e77f3bdd9066fd714419
Author: car <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 49ca32d8c587c7fee72546097bb219c80ad10be7
Author: car <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 ac7d7fb6419ace3a862cc5518aadcfa06f921393
Author: car <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 25803efb44659888162eb5c82470b70c5c3d9d42
Author: car <car>
Date:   Wed May 26 13:05:51 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/.cvsignore

commit 846c4a6c05a1b37562a86086b5892c4e7fd16ced
Author: car <car>
Date:   Wed May 26 13:01:39 2004 +0000

    *** empty log message ***

Src/F_BaseLib/test/.cvsignore
Tests/F_BaseLib/.cvsignore

commit 27476ffcd758534f9c4bb82611c3dc32b8e60f5d
Author: car <car>
Date:   Wed May 26 13:01:39 2004 +0000

    *** empty log message ***

Tests/F_BaseLib/.cvsignore

commit e7e34a1713e1fb922ac8ceb35248f50b1abafa47
Author: car <car>
Date:   Tue May 25 22:39:51 2004 +0000

    *** empty log message ***

Src/F_BaseLib/multifab.f90
Src/F_BaseLib/test/main.f90
Src/LinearSolvers/F_MG/mg.f90
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak

commit 9ddfb55b9f61468cfeebcbf24b4a84ff6a72361e
Author: car <car>
Date:   Tue May 25 04:27:55 2004 +0000

    module name mismatch

Src/F_BaseLib/bl_parmparse.f90

commit ba98df7da8e59a7650a48ed9ce79dad861035866
Author: car <car>
Date:   Tue May 25 04:12:59 2004 +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 3772518ef91fb00b9df7ef2646954a662fffbe0e
Author: car <car>
Date:   Tue May 25 04:03:19 2004 +0000

    missed bl_parmparse.f90

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/NPackage.mak

commit 0f18e2ea821ac052e112407ac4db5295b202525a
Author: car <car>
Date:   Tue May 25 02:00:45 2004 +0000

    aux-->extern

Src/LinearSolvers/F_MG/GPackage.mak

commit 7d77ea17736f29e19cc8ce5334c7edb13f453941
Author: car <car>
Date:   Mon May 24 22:58:04 2004 +0000

    f90doc; mostly ignore for now

Src/F_BaseLib/test/main.f90
Tests/F_BaseLib/main.f90
Tools/F_mk/GMakedefs.mak
Tools/F_mk/GMakerules.mak
Tools/F_scripts/f90doc/expr_parse.pl

commit 4593ddec793ac374919107352479c519a75b9b68
Author: car <car>
Date:   Mon May 24 22:40:52 2004 +0000

    add f90doc; you never know

Tools/F_scripts/f90doc/README
Tools/F_scripts/f90doc/expr_parse.y
Tools/F_scripts/f90doc/f90doc
Tools/F_scripts/f90doc/htmling.pl
Tools/F_scripts/f90doc/stmts.pl
Tools/F_scripts/f90doc/typing.pl
Tools/F_scripts/f90doc/utils.pl

commit bb2d379c65580d996ce45c93cd8e25bfc62ef3ff
Author: car <car>
Date:   Mon May 24 22:32:37 2004 +0000

    *** empty log message ***

Src/F_BaseLib/NPackage.mak

commit 711dfa1b0248f32cd0804287b510946799c2acff
Author: car <car>
Date:   Mon May 24 22:25:41 2004 +0000

    *** empty log message ***

Tools/F_mk/NMakedefs.mak
Tools/F_mk/NMakerules.mak

commit 54393fd3ea15a88ac5f4f930ac78a589f96deeae
Author: car <car>
Date:   Mon May 24 22:11:02 2004 +0000

    *** empty log message ***

Src/F_BaseLib/GPackage.mak
Src/F_BaseLib/bl_mem_stat.f90
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 0031d6c45fae24aef51d743870d85ecec81321ff
Author: car <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 a86f9ca50f60b35942beb7d742c633c61fa8d590
Author: car <car>
Date:   Mon May 24 21:59:14 2004 +0000

    *** empty log message ***

Tools/F_scripts/ibm_sp_batch.poe

commit b3d55561dfd2d51a821f8fb56c0a4d6230ed386e
Author: car <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
Src/F_BaseLib/bl_utility.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/f2kcli.f90
Src/F_BaseLib/f2kcli_nag.f90
Src/F_BaseLib/f2kcli_win32.f90
Src/F_BaseLib/f2kgetcl.c
Src/F_BaseLib/fab.f90
Src/F_BaseLib/fabio.f90
Src/F_BaseLib/fabio_c.c
Src/F_BaseLib/interp.f90
Src/F_BaseLib/knapsack.f90
Src/F_BaseLib/layout.f90
Src/F_BaseLib/list_box.f90
Src/F_BaseLib/mboxarray.f90
Src/F_BaseLib/mpi.f
Src/F_BaseLib/mt19937ar.f90
Src/F_BaseLib/multifab.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/pingpong.f90
Src/F_BaseLib/plotfile.f90
Src/F_BaseLib/ppm_util.f90
Src/F_BaseLib/ppm_util_c.c
Src/F_BaseLib/sort_box.f90
Src/F_BaseLib/sort_d.f90
Src/F_BaseLib/sort_i.f90
Src/F_BaseLib/test/GNUmakefile
Src/F_BaseLib/test/conn_defs
Src/F_BaseLib/test/inputs.domain
Src/F_BaseLib/test/knapsack.out
Src/F_BaseLib/test/main.f90
Src/F_BaseLib/test/t_main.f90
Src/F_BaseLib/timer_c.c
Src/F_BaseLib/vector_i.f90
Src/LinearSolvers/F_MG/GPackage.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_smoother.f90
Src/LinearSolvers/F_MG/sparse_solve.f90
Src/LinearSolvers/F_MG/stencil.f90
Src/LinearSolvers/F_MG/stencil_nodal.f90
Tests/F_BaseLib/GNUmakefile
Tests/F_BaseLib/conn_defs
Tests/F_BaseLib/inputs.domain
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_mk/GNUmakefile
Tools/F_mk/NMakedefs.mak
Tools/F_mk/makefile
Tools/F_scripts/moddep.pl
Tools/F_scripts/tcsort.pl

commit 9188eec0a9100f94ece80c239dc9c2fbc576b052
Author: car <car>
Date:   Mon May 24 21:50:06 2004 +0000

    Initial revision

Tests/LinearSolvers/F_MG/regression
Tests/LinearSolvers/F_MG/t_smoother.f90

commit 72e2fea092182e0c9a0045f119d2145ffd044352
Author: vince <vince>
Date:   Fri Apr 30 21:11:23 2004 +0000

    index type fix.

Src/C_BaseLib/BoxList.cpp

commit c2a1202df53ab577d766f8db2aa71ac4438d128c
Author: car <car>
Date:   Tue Apr 27 17:04:05 2004 +0000

    no longer builds by default

Src/C_BaseLib/GNUmakefile

commit 90cbcc3b44b5cac1bae0d5ced9dd7a19c313ee17
Author: car <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 5f71ba225886f5e9a9eddfb3672eda7010895de2
Author: car <car>
Date:   Wed Mar 31 23:18:22 2004 +0000

    some checks for vismf file correctnes

Src/C_BaseLib/VisMF.cpp

commit 4c6a74e9beda87701a774bd97ba3fb0833293872
Author: almgren <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 b9db64809097bae36f1179609a91ad8e1af7f298
Author: almgren <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 62d7514c41b65dcecbf5e6aef40e66a6fd4ce516
Author: car <car>
Date:   Tue Mar 9 18:35:37 2004 +0000

    PathScale support

Tools/C_mk/Make.Linux

commit 1045ed89e9d43b8ad46d768c89f10bdede7d3a34
Author: car <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 ffa6f543158bf0709d571781bbb6cd7c905e0384
Author: car <car>
Date:   Mon Mar 8 23:06:36 2004 +0000

    swap is never defined, but declared

Src/C_BaseLib/Array.H

commit b4e583ee857d14fa1a6f09caeafb2737cf205b7e
Author: car <car>
Date:   Fri Mar 5 17:53:30 2004 +0000

    obsolete

Src/C_BaseLib/test/tThread.cpp
Tests/C_BaseLib/tThread.cpp

commit 2c011e36359fa0e1f7037e4511636cb57a8f67b5
Author: car <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 df9670ac7876c4730934c4b709bd6849565a2315
Author: car <car>
Date:   Thu Mar 4 18:09:40 2004 +0000

    PathScale

Src/C_BaseLib/FPC.cpp

commit fb1ad123abea9559bcd0dfca7b003afdb1c39cde
Author: car <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 e4a715a0c9a616cf3bff33cf582ccd5559a77922
Author: car <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 f13c8185f03d341f0e66a28a399cb863762799a5
Author: car <car>
Date:   Thu Feb 19 18:17:54 2004 +0000

    valgrind: tuples constructors have default values

Src/C_BaseLib/Tuple.H

commit 401c316989f8b13693735ba61c889077b237a1ea
Author: car <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 db3bf8ceabb41b1db3de4254ab130cc0699b8285
Author: car <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 d059e242adc76142fa5a6998bfa41b375f5a8d32
Author: car <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 ec32d1051eb34573f270aa5aa870aa6fb8319969
Author: lijewski <lijewski>
Date:   Wed Jan 21 21:04:13 2004 +0000

    First version.

Src/C_BaseLib/test/tParmParse.cpp
Tests/C_BaseLib/tParmParse.cpp

commit 089404b821847ef4abbf3b09ae238977305e24ce
Author: lijewski <lijewski>
Date:   Tue Jan 20 21:54:10 2004 +0000

    Added tParmParse

Src/C_BaseLib/test/GNUmakefile
Tests/C_BaseLib/GNUmakefile

commit c8721639f57de7c22ace34592325d8ecf10117b4
Author: lijewski <lijewski>
Date:   Tue Jan 20 21:53:31 2004 +0000

    fixed bug

Src/C_BaseLib/ParmParse.cpp

commit 3c0a35e70679cfa3842ed52450028f466691b2da
Author: car <car>
Date:   Wed Jan 7 21:45:03 2004 +0000

    tweak for std::size_t

Src/C_BaseLib/winstd.H

commit 5d62ad51712f6c8c8f3fe25f93370b8086274c74
Author: car <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 f207e31aaea2e9cf74471161c1eb82bda85af545
Author: car <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 d262d75544068ba4aa663fe2a8622769ead9ff99
Author: car <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 9e280b84180e490274baf6576b0b2725a0c2f12f
Author: car <car>
Date:   Mon Dec 8 23:13:46 2003 +0000

    powerpc for BGL

Src/C_BaseLib/FPC.cpp

commit 659bbddd63acd9cc6ee51135b94dc81eb9a34b4a
Author: marc <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 9b13c5691837d8676c6ac8023de32762b75ff9e6
Author: lijewski <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 72bda6b604d5ca106b815cdc75e549b63d18c02a
Author: almgren <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 1df444b492c3aa79f3cfe40e6a79f6b000c7fb1a
Author: lijewski <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 864d92fc3c726cdd973e7c93ba56c692ae2f0abb
Author: lijewski <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 624f352c2a4adf085c77b42e118234ea149c3439
Author: lijewski <lijewski>
Date:   Mon Sep 8 21:07:45 2003 +0000

    Make tags declaration & call of buffer() consistent.

Src/C_AMRLib/Amr.cpp

commit 19e1f90515f92391414728ac2a08dc4acf6b6cbb
Author: car <car>
Date:   Thu Aug 28 17:17:27 2003 +0000

    __amd64__

Src/C_BaseLib/FPC.cpp

commit 9fabc6e22a40bd508462d628e19c53b9b31367f6
Author: car <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 4c7102f2f4c9186a3468ff98ed24db0effdaa3a5
Author: lijewski <lijewski>
Date:   Thu Aug 14 22:26:57 2003 +0000

    some cleanup

Src/C_AMRLib/TagBox.cpp

commit 7873006852ec9aa9187bd6b5ed0cb1a22b9902e5
Author: lijewski <lijewski>
Date:   Thu Aug 14 19:18:14 2003 +0000

    minimized comm costs in collate()

Src/C_AMRLib/TagBox.cpp

commit 791ed94cd5028904482a203d62df92841a5ffea2
Author: lijewski <lijewski>
Date:   Wed Aug 6 21:04:01 2003 +0000

    added -cm to Intel Fortran

Tools/C_mk/Make.defs

commit 48ce640fcdebf6342958665df5f77978d7af6d3f
Author: car <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 780821817df97be36693006043ab4eb7b1209d8b
Author: lijewski <lijewski>
Date:   Mon Jul 21 21:22:26 2003 +0000

    First cut -- can parse chemkin & therm files.

Tools/C_scripts/ckread.pl

commit 4d9f8bdd5794bd1429e782a8f9265101d8ff21f4
Author: lijewski <lijewski>
Date:   Fri Jul 18 04:57:11 2003 +0000

    Gather -> Alltoall

Src/C_AMRLib/FluxRegister.cpp

commit cbbf9a8608e9d261418692e105ad4d603879f3b3
Author: lijewski <lijewski>
Date:   Fri Jul 18 04:51:46 2003 +0000

    Gather -> Alltoall

Src/C_BaseLib/FabArray.H

commit 849a1cfc73520c7f6271bf761a67b3aaa4e5543a
Author: car <car>
Date:   Tue Jul 8 20:48:23 2003 +0000

    cleanup

Src/LinearSolvers/C_TensorMG/visc2d.m

commit 961dbf10bbc06cf974cd5f73a769a69d0c3bd207
Author: car <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 4c74c18df0471b4158bae9acb8e8b75ed5343508
Author: car <car>
Date:   Tue Jul 8 20:04:02 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/visc3d.m

commit f1ca27135358d4760fa650826d0114a23ca34c84
Author: car <car>
Date:   Tue Jul 8 19:42:33 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/visc3d.m

commit dd8fe0f0d13400261a1f44060849b966c19c410e
Author: car <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 51838d94594079c4ad6e2b4ffa884cc31553d21d
Author: car <car>
Date:   Sat Jul 5 15:22:30 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_TensorMG/Format.m

commit 751872b8c14a09307b6259ae4f4a71a8ea9235f8
Author: car <car>
Date:   Fri Jul 4 21:58:36 2003 +0000

    Mathematica 5.0 fixes

Src/LinearSolvers/C_TensorMG/Format.m

commit 2797519e34993f7635ba8eb5b3a6fde42b6316cb
Author: car <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 978e2e0ccd2d1d3c1744139b955560c52c45e31a
Author: lijewski <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 9cdbf85b45ac7e253763172cb796e39b92456720
Author: car <car>
Date:   Fri Jun 20 19:37:11 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.IRIX64

commit 894dda803579c9f9d707faaa0282c2f1c1f3d7d4
Author: car <car>
Date:   Fri Jun 13 22:03:23 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.H

commit 87c256510cac08738a0705ef7d131127d34e78bd
Author: car <car>
Date:   Fri Jun 13 19:50:47 2003 +0000

    inline out of order

Src/LinearSolvers/C_NodalMG/interface.H

commit 2b5f729ed3d38979c3948d6cd8cfef3b15ca765d
Author: car <car>
Date:   Wed Jun 4 21:41:56 2003 +0000

    redhat 7.1 fortran

Tools/C_mk/Make.defs

commit 75fae46b373d039b59e1737b80e2ccc0498808cd
Author: vince <vince>
Date:   Wed May 21 22:47:52 2003 +0000

    fix for escher

Tools/C_mk/Make.defs

commit 9a913c10cdf86a576e9c2221a180d5ca4874c99c
Author: vince <vince>
Date:   Wed May 21 22:47:13 2003 +0000

    fix for escher.

Tools/C_mk/Make.IRIX64

commit be3e3f2ae39862cff5033264db8ee893254761ea
Author: lijewski <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 37ec404c770ddccb43ba0eb198478ed8666c4266
Author: car <car>
Date:   Fri Apr 11 17:16:06 2003 +0000

    redhat 7.1

Tools/C_mk/Make.defs

commit f5c066460fb717acf68599635c3eb9adae4cb4bd
Author: marc <marc>
Date:   Wed Apr 9 22:35:24 2003 +0000

    change constant to a long

Src/C_BaseLib/DistributionMapping.cpp

commit b02f7e8c8aa94edb459b611978f1b17d95d79de5
Author: car <car>
Date:   Thu Apr 3 18:44:31 2003 +0000

    flush at end of grid log entry

Src/C_AMRLib/Amr.cpp

commit 3feeeb5a3749796da87b4ad30265bfea2f52f12b
Author: marc <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 9d325f6fa8a88820f1abecb1b75fe8833488cdf0
Author: lijewski <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 8d41e77f991885b174724725e732afcbf07d3a35
Author: lijewski <lijewski>
Date:   Wed Mar 12 20:54:59 2003 +0000

    fixed divide by zero in verbose output

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 6273326212c47219d713293ea608b0d0d22ff790
Author: lijewski <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 9c53dfad1edf4d9c22a089c23a24af8015071dff
Author: lijewski <lijewski>
Date:   Fri Mar 7 16:59:25 2003 +0000

    ParmParse'd in max_efficiency

Src/C_BaseLib/DistributionMapping.cpp

commit 552146a99f23e69989854b73c4db8c86d3e7640f
Author: lijewski <lijewski>
Date:   Thu Mar 6 23:57:38 2003 +0000

    wrapped knapsack times in verbose

Src/C_BaseLib/DistributionMapping.cpp

commit 214d8c775da2c484e736bfa2c6881bbed9bddedc
Author: lijewski <lijewski>
Date:   Thu Mar 6 22:34:56 2003 +0000

    print out some knapsack() timings

Src/C_BaseLib/DistributionMapping.cpp

commit 9dd333dd4709669a48315e5dbf228c7905db4665
Author: lijewski <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 db9705b152febf75915c8a2ef137703121f36d84
Author: lijewski <lijewski>
Date:   Wed Feb 26 18:07:08 2003 +0000

    added verbose option

Src/C_BaseLib/DistributionMapping.cpp

commit 778f752b6b6d5443fa185097411cdf32616346a3
Author: car <car>
Date:   Fri Feb 21 22:49:10 2003 +0000

    compiles, probably doesn't work in parallel

Tools/C_mk/Make.defs

commit 6df40a13f2509445713c26029711cc425f8c3411
Author: almgren <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 633035140ac1dfa9c699f0897ea373674f5faf9d
Author: almgren <almgren>
Date:   Tue Feb 18 21:13:18 2003 +0000

    Removed all calls to writeMF.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit a86c54ee1211e2424b487b85bbea3b57c0a48b47
Author: car <car>
Date:   Tue Feb 18 20:55:00 2003 +0000

    strstream -> sstream

Src/C_AMRLib/AmrLevel.cpp

commit cc1684ef0c093ee002ce759583a0dcd89dd38c4a
Author: car <car>
Date:   Tue Feb 18 20:54:40 2003 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/ABec_UTIL.F

commit fc0b74a760e477f21b7299bffc562a78de0d6e1b
Author: car <car>
Date:   Wed Feb 12 22:31:53 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 04b205ee4cf423c05e4975ce0504616c4ebbd24e
Author: car <car>
Date:   Wed Feb 12 22:31:12 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit b16410aaba28bd9f7409ba6c0f769f5c57bde927
Author: car <car>
Date:   Fri Feb 7 17:42:26 2003 +0000

    minor problem, periodic fillpatch

Src/C_AMRLib/AmrLevel.cpp

commit b1244a917f23e2ae605ff6659d552b785ab747b2
Author: car <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 b972d0560963871df814e2a346e2bf72aa3f3087
Author: lijewski <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 75b24134e7d7f556b9070b610700b3c49754c7b2
Author: car <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 8b69b749ab9f3351a3ab636e133425e4893a3b91
Author: marc <marc>
Date:   Tue Jan 28 20:55:35 2003 +0000

    Modernize lib builder

Tools/C_scripts/dsp.lib.mak

commit a6fd45d7208593fc14a69b4535dc19ba384bfdc4
Author: car <car>
Date:   Mon Jan 27 17:10:36 2003 +0000

    bl_pd_is_ioproc

Src/C_BaseLib/ParallelDescriptor.cpp

commit e20040e185d6c526c4c2f12fe3daabe3cea4ced9
Author: car <car>
Date:   Thu Jan 23 20:10:01 2003 +0000

    win32 hates templates

Src/C_BaseLib/BaseFab.H
Src/C_BaseLib/BaseFab.cpp

commit 2840e4494233aebbfde098778dc1f0ff922e5d0b
Author: lijewski <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 9f34392395196807be6388ea2cb7557c45401567
Author: car <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 f53ef7678ab59f93f9c5016912b46a3e7b13d8cb
Author: car <car>
Date:   Fri Jan 3 19:25:11 2003 +0000

    foolish mistakes

Src/C_BaseLib/BLParmParse_F.f
Src/C_BaseLib/ParmParse.cpp

commit e794af81264b3e7382fb7dd4ba3bba6b820eaf57
Author: car <car>
Date:   Thu Jan 2 22:30:26 2003 +0000

    libpthread

Tools/C_mk/Make.Linux

commit 3fb32b456a1bf26773498b24f7149cee32b08732
Author: car <car>
Date:   Thu Jan 2 14:59:30 2003 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.defs

commit 5e83e8d74b427ef8d5ab948fece11e31bcdda2fd
Author: almgren <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 b64082d2275e9504c433a5b405c08a833f90931a
Author: car <car>
Date:   Fri Dec 20 23:05:39 2002 +0000

    fix for FluxRegister::ADD

Src/C_AMRLib/FluxRegister.cpp

commit 7a86d45ec62e0b70ea7f95f5c1a59d4fbf8f3698
Author: lijewski <lijewski>
Date:   Wed Dec 18 18:44:23 2002 +0000

    fixed comment

Src/C_BaseLib/FabArray.H

commit 60b4a0589ac33ddd7ba7c45ab32754a82812cbb8
Author: almgren <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 b9997d434614be6fecd1ecbe6a9b84b90bfa8442
Author: almgren <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 824afb82c6ba1026397fc6eff3d9c3e1e162db0b
Author: almgren <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 f6e5c3a495b1b8b495b2f576493e155655dcddfe
Author: lijewski <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 b7fedf0598fcf4e80ee1586da8b4247ca4bfb7c4
Author: lijewski <lijewski>
Date:   Tue Dec 10 20:31:14 2002 +0000

    Commented out HeaviestCPU() stuff used by MinimizeCommCosts().

Src/C_BaseLib/DistributionMapping.cpp

commit 4775084afeb993165696d35a27ffeda60714a013
Author: lijewski <lijewski>
Date:   Sat Dec 7 16:25:26 2002 +0000

    fixed syntax error

Src/C_AMRLib/INTERP_3D.F

commit 44a39427269360a2fb8e6d575ae0fcb6c7707ec9
Author: lijewski <lijewski>
Date:   Sat Dec 7 16:09:16 2002 +0000

    increased the cache hit rate

Src/C_BoundaryLib/FabSet.cpp

commit 75b430922240f134c7e9b543d057ef1c2379ff20
Author: almgren <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 a744aa1a34c9040599833037285d25c83e5d6795
Author: almgren <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 2fce9df1eadb5f904621e8ab09474aecc69df3a8
Author: lijewski <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 39dcc0a59d929b80056e7b31934241c6de224e7d
Author: lijewski <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 8e57f0e75bc1d92bad5ad434e7010833fc3aba9a
Author: lijewski <lijewski>
Date:   Tue Dec 3 18:03:27 2002 +0000

    improved FillBoundary cache hit ratio

Src/C_BaseLib/MultiFab.cpp

commit e4de0f67f29d7ce7df938359e79fb568586dc7e3
Author: lijewski <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 008d49a5d4ddd8f88b12242433570725b4cc3ac8
Author: jbb <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 579fe9bbd1c4c96367b5566f01551e6c11dd7270
Author: car <car>
Date:   Fri Nov 29 22:12:18 2002 +0000

    no trailing semicolons

Src/C_BaseLib/SPECIALIZE_F.H

commit 066515e99d39ad930b40fe06abb3daf6ef97fcc9
Author: car <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 358de07df1e9bd23fe7afe65cbe3a0b244344116
Author: lijewski <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 6704ac5bd8e29a3168c860b5d261ad3ab178af2b
Author: lijewski <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 897b54c6dcb4b5e2ae68cc6b69d80e8e66ced5fe
Author: lijewski <lijewski>
Date:   Wed Nov 20 16:55:55 2002 +0000

    additional arg to compFlux()

Src/LinearSolvers/C_CellMG/ABecLaplacian.H

commit 4a25a28f3499c50c0d4ea219af747d2cfbb2f46f
Author: lijewski <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 55969ce784ca55e01aec8f0dafeb74e79740125c
Author: lijewski <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 00be8fe22bcc571d1c57b48e71086b3b59523bb2
Author: lijewski <lijewski>
Date:   Thu Nov 14 21:13:08 2002 +0000

    removed statics from template functions

Src/C_BaseLib/FabArray.H

commit 52c3cd0f97c04b48f55e9188fc2c35c8a476decb
Author: car <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 e3729d0a2c222d292de922cd727b02361fa6e220
Author: marc <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 944dd6e27f96ec5e8ec6db5cab2f33d73c68e935
Author: marc <marc>
Date:   Thu Nov 14 00:13:23 2002 +0000

    fix Mikes extra arg fix

Src/C_AMRLib/AmrLevel.cpp

commit 8c1d3054516982bf53570db1eb06d96137b00241
Author: lijewski <lijewski>
Date:   Wed Nov 13 17:15:20 2002 +0000

    quiet valgrind

Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp

commit 0e6e765cf2025d0ff5d9d54933c3945f8f86e59f
Author: lijewski <lijewski>
Date:   Wed Nov 13 05:04:58 2002 +0000

    tad rearrangment

Src/C_AMRLib/AmrLevel.cpp

commit 43c724d14aba7845a1af1c9a48971505168c36bf
Author: lijewski <lijewski>
Date:   Tue Nov 12 20:49:35 2002 +0000

    to shut up valgrind

Src/C_BaseLib/PArray.H

commit a330d19e00eaae217b6faf8c983e00f57f0e3f3c
Author: lijewski <lijewski>
Date:   Tue Nov 12 17:08:48 2002 +0000

    fixed mismatched deltes

Src/C_BoundaryLib/InterpBndryData.cpp

commit 2d155f78b6e2786de6d3e2aa95d59a64f323be42
Author: lijewski <lijewski>
Date:   Mon Nov 11 17:49:53 2002 +0000

    can now do some semblance of tracing

Src/C_BaseLib/BLProfiler.cpp

commit 748ce3a8dc118a795add90178487df143e0695b6
Author: almgren <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 887668fae80b6a66f3c93e82190aa0757db25ad7
Author: lijewski <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 b7c0562e2a0cb5f73cb98c7dbadac4b95c042d59
Author: lijewski <lijewski>
Date:   Fri Nov 8 22:00:51 2002 +0000

    added some BL_PROFILE()s

Src/C_AMRLib/Interpolater.cpp

commit 0660a6fb33edbd784fc51f11337bab2c5710a10a
Author: car <car>
Date:   Fri Nov 8 18:34:42 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/lo_bctypes.fi

commit dd76c9ff44fd4ee97b946c6a563bda77d60ad74d
Author: lijewski <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 29740f5716a65d8ec46082d6cb0005900aad09ae
Author: lijewski <lijewski>
Date:   Wed Nov 6 20:51:41 2002 +0000

    tad bit o cleanup

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 051df1e02cdbfe0126797f71064b1ecc969c0d4d
Author: almgren <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 0a6368d0066e23bac7eb8d9692f61d3586d7cbe1
Author: lijewski <lijewski>
Date:   Tue Nov 5 21:06:17 2002 +0000

    +K2 -> +K1

Tools/C_mk/Make.AIX

commit b0498c697354ed04e8627461335bbec506c0cd97
Author: lijewski <lijewski>
Date:   Tue Nov 5 05:34:21 2002 +0000

    removed extraneous end do

Src/C_AMRLib/INTERP_3D.F

commit 9a4ea298a0cb1b7c485989f594421473c40c23c3
Author: almgren <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 696eb878682bcbadaf707559045548ba4eb27cca
Author: almgren <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 15bd466933453dbc08f5fd104a1a7acca579a099
Author: lijewski <lijewski>
Date:   Thu Oct 31 21:59:21 2002 +0000

    Added -qrtti=all when debugging.

Tools/C_mk/Make.AIX

commit 570d074f89552d9c351ac326cf540c6f4b71433b
Author: lijewski <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 0b2e08c3e78ddb591e7328bc6785e19d87eaa224
Author: lijewski <lijewski>
Date:   Thu Oct 31 21:01:30 2002 +0000

    removed excess profiling gunk

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 204689191bcbea32cd97cff4692ccb362ab058ae
Author: car <car>
Date:   Thu Oct 31 18:44:00 2002 +0000

    fixes for microsoft

Src/C_BaseLib/ParallelDescriptor.H

commit 7d9981e4eaf04618e237096ddce425436b680318
Author: car <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 ee3920ae5c05727b2e548550cac08faba0b30cc7
Author: lijewski <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 4118f6ed547d7d7a5217fdd8be69e285b627486b
Author: lijewski <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 6513a8713e176428a29ba9a505b5b9d8cae452da
Author: lijewski <lijewski>
Date:   Fri Oct 25 22:21:44 2002 +0000

    speed improvements

Src/C_BaseLib/Utility.cpp

commit 36133143305506193bd7629ea1ae1835cd2ff2dd
Author: lijewski <lijewski>
Date:   Thu Oct 24 21:56:00 2002 +0000

    added InvNormDist stuff

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit d46b86c2a8729643c3fcde8ed93318d341112d1d
Author: car <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 0c218e12d0e07dc4588d2de4b1da86e94849f7bc
Author: almgren <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 5fbcd19215eac08f651e59bc69cae310e7d556cc
Author: car <car>
Date:   Fri Oct 11 18:20:44 2002 +0000

    improved error message

Src/C_BaseLib/BLProfiler.cpp

commit 75131d9d2b22e2211d1fc94b8b1df2d0fec52eeb
Author: car <car>
Date:   Fri Oct 11 18:20:29 2002 +0000

    profiling fix

Src/C_AMRLib/TagBox.cpp

commit da6e0aeb92c1a06750482642d2b4f9955bcd8b26
Author: car <car>
Date:   Fri Oct 11 13:28:27 2002 +0000

    more profiling

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/StateData.cpp

commit 936891308870208576b08caa0ecf06da6ba04c3e
Author: car <car>
Date:   Wed Oct 9 21:43:20 2002 +0000

    *** empty log message ***

Src/C_AMRLib/Interpolater.cpp
Src/C_AMRLib/StateData.cpp

commit dc6edee98a6b91b43bb0b48dd3957858c6db49d9
Author: car <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 3d07018f200bd461e76b42c2304390bc0d984bd8
Author: vince <vince>
Date:   Tue Oct 8 21:33:28 2002 +0000

    added ,n to a few crse reference.

Src/C_AMRLib/INTERP_3D.F

commit 00be673828edd379e0b6cc6f8866166575b0e71a
Author: almgren <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 49b8e5e832f378344fd4c6af56b6836c1faa99ed
Author: lijewski <lijewski>
Date:   Mon Oct 7 20:28:10 2002 +0000

    remove MISMATCH stuff ...

Src/C_AMRLib/INTERP_2D.F

commit b7908824111efc7162e974fe7a9b1b7170f3fbec
Author: car <car>
Date:   Sun Oct 6 18:02:43 2002 +0000

    more profiling

Src/C_BaseLib/DistributionMapping.cpp

commit c6899428eff72a736d516bbcc22e7e35ec4bf22b
Author: car <car>
Date:   Wed Oct 2 22:26:12 2002 +0000

    silence some warnings

Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f

commit 85ac3844ed25efacd5b61af758b6d79fb7bbe3cf
Author: marc <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 d5465d489018dc84add2eacad0f83371ca5d2fcf
Author: lijewski <lijewski>
Date:   Tue Oct 1 22:38:42 2002 +0000

    ensure sprintf() buffer big enough

Src/C_BaseLib/Utility.cpp

commit 775d87c9115b151d3c09d46fc288790a60b4e602
Author: lijewski <lijewski>
Date:   Sat Sep 28 19:03:35 2002 +0000

    silenced compiler warnings

Src/C_AMRLib/Interpolater.cpp

commit e34c2c2cf5e8f13a85147150e96e25894c3de450
Author: lijewski <lijewski>
Date:   Sat Sep 28 19:03:07 2002 +0000

    bug fix for AIX

Src/C_AMRLib/INTERP_F.H

commit 79831cdf82191f3425b30839f7789cb4bac775fb
Author: almgren <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 08ed79196b188b0804d9a993a542055ada631c33
Author: lijewski <lijewski>
Date:   Mon Sep 23 19:06:21 2002 +0000

    *** empty log message ***

Tools/C_scripts/compressor

commit 0a456eb72b474179ebee79759de5abb2e0d2a9fd
Author: car <car>
Date:   Mon Sep 23 17:02:45 2002 +0000

    compressor has a lock file

Tools/C_scripts/compressor

commit 5447a6f1e4b9cf53ac51598ac9fe4db9bd52fd32
Author: car <car>
Date:   Mon Sep 23 16:57:36 2002 +0000

    testing new compressor

Tools/C_scripts/compressor

commit d4bc55bdc1e5c2e63d2dafad84ea4a2d0a727976
Author: car <car>
Date:   Thu Sep 19 21:02:14 2002 +0000

    do'h

Src/C_BaseLib/Utility.cpp

commit b3e6473b590dcd7439c428d358f66a85d80128a9
Author: car <car>
Date:   Thu Sep 19 19:26:22 2002 +0000

    fort call to initrand

Src/C_BaseLib/Utility.cpp

commit 5f282fb4f987f61dfde1528afb54242e5210fc38
Author: lijewski <lijewski>
Date:   Fri Sep 13 19:19:41 2002 +0000

    Added MinimizeCommCosts()

Src/C_BaseLib/DistributionMapping.cpp

commit 5034bb0138f087d92b96901b98a4915dd3a7549b
Author: car <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 7322f3b27672b1e1dd9c4095070696788022de56
Author: car <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 1819256d67f00e195e992d240b8f9726f1119997
Author: car <car>
Date:   Tue Sep 10 18:25:27 2002 +0000

    oops

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit f8044c77b4caa12970e04217e96d029cb0fa05ff
Author: car <car>
Date:   Tue Sep 10 18:19:57 2002 +0000

    more debugging output

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 847c4f1505a8a2100719a7f933e41529753bb570
Author: car <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 19da89cb6efee2ad7a61abbaa3e7348d0dd3e2a0
Author: car <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 208b9aca634040c9e82a5d610593b8e3ebf39f48
Author: marc <marc>
Date:   Mon Sep 9 22:30:33 2002 +0000

    remove __kcc... define-it breaks compiles on brainerd

Tools/C_mk/Make.defs

commit 3581d402e37a971303f7dc4a02348701a1c376cf
Author: car <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 38e1e3f54051608ab55c82c7f699310770fc6d77
Author: car <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 c6ea945bb58d0727fa2a5d6f1a7eed102ed4b567
Author: car <car>
Date:   Thu Sep 5 20:59:10 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.f

commit 6fb4cd6848bd27570a6580a07ae35478e5c1abc7
Author: car <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 23797562c934cee3d5ee1c8c1080e4acde9b6890
Author: car <car>
Date:   Wed Sep 4 15:29:53 2002 +0000

    use .f not .F

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 14bffb1f8811f3bf03d58670ab6c1113e00a6419
Author: car <car>
Date:   Tue Sep 3 19:07:05 2002 +0000

    left in some debugging cruft

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 7a8b14e59eab6001b5cae5870d02798f05fa127b
Author: car <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 5e3d91828e01c26bd133ca92ff8a004cc36cefff
Author: car <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_real2d.f
Src/LinearSolvers/C_NodalMG/amr_real3d.F
Src/LinearSolvers/C_NodalMG/amr_real3d.f
Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg2d.f
Src/LinearSolvers/C_NodalMG/hg_avg3d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d.F
Src/LinearSolvers/C_NodalMG/hg_multi2d.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_multi3d.F
Src/LinearSolvers/C_NodalMG/hg_multi3d.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F
Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f
Src/LinearSolvers/C_NodalMG/hg_proj2d.F
Src/LinearSolvers/C_NodalMG/hg_proj2d.f
Src/LinearSolvers/C_NodalMG/hg_proj3d.F
Src/LinearSolvers/C_NodalMG/hg_proj3d.f

commit 42a522787627f88f64e4e14bfc6541d7787ed3f1
Author: car <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 a8c3f02ff1d95e595e1362a92c673c22727d3aa7
Author: lijewski <lijewski>
Date:   Fri Aug 30 22:10:34 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 2c8b4056b4659d898c70c7ee3d27c939b8e10609
Author: car <car>
Date:   Thu Aug 29 22:17:09 2002 +0000

    silence a warning on int<>bool

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 8dcd752f481a86bfeabf2dc85a313fd0bf985161
Author: car <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 ba83b7e833192cdaf9b9762f1069f342410c1a16
Author: car <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 c28d1a56289affb5e3e08426102daf3c912ecf48
Author: car <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 16a42923753f080498a239df912dc65be81fe592
Author: lijewski <lijewski>
Date:   Tue Aug 20 21:00:55 2002 +0000

    Increased data size ...

Tools/C_mk/Make.AIX

commit d7c16d60054c0be5a05e8b14710cb9c8f758be48
Author: car <car>
Date:   Fri Aug 16 23:15:27 2002 +0000

    change infinity from e20 to e200

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 6a92d11f7d6e899fd8b1b535691d7b20a560ab03
Author: car <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 567805711c7d63fc624cc899ae90d000ec1ace9f
Author: car <car>
Date:   Wed Aug 7 17:23:56 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit d2c3c81096e73a6291ebf8a14b546dcb946d4657
Author: car <car>
Date:   Tue Aug 6 18:09:06 2002 +0000

    *** empty log message ***

Src/C_AMRLib/AmrLevel.cpp

commit b9619730801951d5484a4af9abce51241fcfb2e8
Author: car <car>
Date:   Mon Aug 5 15:41:22 2002 +0000

    remove intel temp files

Tools/C_mk/Make.rules

commit c0c667d7c9110d495d3f5ca819f72271058b023e
Author: lijewski <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 dc8e9304dd720584c470e9a04b99f3d6f385e348
Author: car <car>
Date:   Wed Jul 24 23:42:57 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit db36f4b41128ff04305bed44765e94455e8b1475
Author: car <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 83f988ef506e23729275a92cc02e69fdd60c7f07
Author: lijewski <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 a7458394c0ec91590ed85ca934e7481461d2f4e5
Author: lijewski <lijewski>
Date:   Fri Jul 12 23:07:38 2002 +0000

    was NOT right

Src/C_BaseLib/DistributionMapping.cpp

commit 4a621026afd2c62c59399f864177130b5c1cc4ee
Author: marc <marc>
Date:   Wed Jun 26 18:06:44 2002 +0000

    Add lf to result file

Tools/C_scripts/dsp.mak

commit 4dcf62268b2f9a5d963c36d8ce8885c7dc31765e
Author: marc <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 fbad2e60697d24e3c1bc5d6d4ecf94669941a2a8
Author: car <car>
Date:   Thu Jun 20 18:28:00 2002 +0000

    another fortran header file

Src/C_AMRLib/bc_types.fi

commit 5bb5ad58fd1c2b06f61c8401b6c33fc54fedd867
Author: car <car>
Date:   Thu Jun 20 15:59:36 2002 +0000

    allow upper/lower case in fortran INCLUDE

Tools/C_scripts/mkdep

commit c7c59d4317e76fa756cb95325de2829ac7a62b88
Author: car <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 2441ee47bae6aa9b5afb7266701d5bba433275d4
Author: car <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 327b5d50c9b29629157a25dcfde098f9090e9234
Author: car <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 d47f72a361995e57ab9cc8df18a11d72c8a6b033
Author: car <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 58d9bd9494a30fce083660b98f757b63758f12c2
Author: car <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 74ab2e60320a660ced82564c3fc95691c4116545
Author: car <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 7e551c8e0e14d43329881299aba71754cac33566
Author: car <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 9b6422265b3b46cd6bedd9d992c753591e43a796
Author: lijewski <lijewski>
Date:   Mon Jun 17 19:36:46 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLParmParse_F.f

commit b9f6ee68d53b6877b47dc065711d8c68718ff143
Author: car <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 3b0ab7d351140defa39d277f958497f87ce3ab37
Author: car <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 1104c57200cc834c4b5681371ca0785690a8ca3f
Author: car <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 fc8382a216c638645962c2d79b1a5b670f117b65
Author: car <car>
Date:   Tue Jun 4 17:42:37 2002 +0000

    Some support for GCC 3.1

Tools/C_mk/Make.defs

commit ada3b90ac2a1f34ba4beb8e5fb6139f070d25449
Author: car <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 7a7ef55bf2b089ff16579041eb47b7980ee3dca3
Author: car <car>
Date:   Wed May 29 22:37:47 2002 +0000

    gcc 3.1 needs to include <iterator>

Src/C_BaseLib/BLProfiler.cpp

commit eecb5589aa4c511e087018914526469522d81087
Author: marc <marc>
Date:   Tue May 28 23:21:12 2002 +0000

    Add a routine to hoextrap to cc

Src/C_AMRLib/FILCC_2D.F

commit 1592396dfb0fac7f68eb3d413b21ba27aa249c09
Author: car <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 5ed76116050a26e1c1c8049bd0b6773bc1b993c4
Author: car <car>
Date:   Thu May 23 19:10:38 2002 +0000

    BoxLib\BLFort.H

Src/C_BaseLib/BLFort.H

commit f9e44ec3453df77a9a85e786d86e90200eb7fd39
Author: car <car>
Date:   Thu May 23 18:22:13 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Make.package

commit 352307f7267e3f2651e4e857bf9009aaebbfecc5
Author: car <car>
Date:   Thu May 23 18:21:48 2002 +0000

    BLFort macros useful for FORTRAN calls

Src/C_BaseLib/BLFort.H

commit 4097b5a7ed6c3f08fd8ef1d75fc9ecdb08bc772c
Author: vince <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 35ed332024ec2f18b72daa9713c55fdb60a6dd7c
Author: lijewski <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 61051ee9955e956d20c98d1d5d4c1eb0aa4456d4
Author: car <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 78a5da48cd0f24917d9ac7542d37e74cafe328cf
Author: marc <marc>
Date:   Sat Apr 27 07:10:24 2002 +0000

    generalize a bit

Tools/C_util/WritePlotFile.H
Tools/C_util/WritePlotFile.cpp

commit 264557add27d7b0fcd10d0b0192c1fa2afb0cd1a
Author: marc <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 88ea98753a8a6a7e25f56dc49f4c42fabb14a8ef
Author: car <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 d5c43512f841a110f05811c865df5208f1c43932
Author: car <car>
Date:   Fri Apr 26 22:24:43 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux
Tools/C_mk/Make.rules

commit 543463b831a75daae8a6959e1ca352a928d7bde2
Author: lijewski <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 e0637cf34b6ebb88cb45f0b5f1d5f5f0578632dd
Author: car <car>
Date:   Wed Apr 24 22:25:20 2002 +0000

    another fix for ICC

Src/C_BaseLib/winstd.H

commit 42b8c0416bb581ddc21b8a9d09ffa8e6dee2ce93
Author: car <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 de124467543d8111597891d8c3f536b5b801df7d
Author: vince <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 d99ba5fe07e2b46cdcbe1f22e0d0902278415c32
Author: vince <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 d37872e6799389542932628aa21f1c4d0478ae71
Author: lijewski <lijewski>
Date:   Tue Apr 16 15:20:28 2002 +0000

    forgot to update LDFLAGS earlier

Tools/C_mk/Make.AIX

commit d17095b45ec6e699248bcadd008e24b7f8611f5b
Author: car <car>
Date:   Mon Apr 15 20:12:26 2002 +0000

    oops

Src/C_BaseLib/BLThread.cpp

commit ba5c805cbbaefc385a630a1a35c8801cbfb0fa0d
Author: car <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 6f84245fbbc3a41dc2e6b217d72940944562b128
Author: car <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 6bf64c777ca95fe0793fc9527bd3970ab7e9bd7c
Author: car <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 17f02da2362d7077d8d269defe3d5fcb8642121c
Author: car <car>
Date:   Mon Apr 8 20:51:36 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Thread.H

commit 7a89f86cc48e7fecf7b5a92b720eaaf1de3817e5
Author: car <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 08d032bb83349780ac1faab95f4d807427346c0a
Author: car <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 4e77108fa360566a6d618f0c567fc6f24eb415fd
Author: car <car>
Date:   Sun Apr 7 17:00:44 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Tools/C_mk/Make.FreeBSD

commit 6e76d0c03f1d46cf110eb6edb1540d7070d56252
Author: lijewski <lijewski>
Date:   Thu Mar 28 21:00:12 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1

commit 67431e34769f1cb0bf183db49ec3e5752dba92d7
Author: car <car>
Date:   Wed Mar 27 23:58:50 2002 +0000

    std::abs on BL_OSF1

Src/C_BaseLib/winstd.H

commit e53fb043a04f24dac3553dace264519dc38048fd
Author: lijewski <lijewski>
Date:   Wed Mar 27 23:49:07 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1

commit e8b74b9591a24e385f16048d27a451aa25e404e1
Author: car <car>
Date:   Wed Mar 27 21:35:59 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.OSF1
Tools/C_mk/Make.mpi

commit 80054ef9b2738152ef362011311cb9772cf9d88d
Author: lijewski <lijewski>
Date:   Wed Mar 27 19:21:54 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 6f68d692ab542621acdaab4253ca9fa87128cad9
Author: lijewski <lijewski>
Date:   Wed Mar 27 17:54:34 2002 +0000

    mods to quiet xlC

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 9aec6659d59ea92930cc0f27e32de52c52a2f77b
Author: lijewski <lijewski>
Date:   Wed Mar 27 17:10:20 2002 +0000

    *** empty log message ***

Src/C_AMRLib/AmrLevel.H

commit c8fa1c422ae811daa0614a0b385cc99c23a1178d
Author: lijewski <lijewski>
Date:   Tue Mar 26 23:59:29 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit f361ea8361ba6f88a6a6858fdc60b41c8f588a7c
Author: lijewski <lijewski>
Date:   Tue Mar 26 22:23:58 2002 +0000

    *** empty log message ***

Src/C_BaseLib/Utility.cpp

commit 420c332ab5552cae6a1e45e17e0b63916e6e06c1
Author: car <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 7c4c5a0c763b437bde265271ab9a7ed8f5aad3e5
Author: car <car>
Date:   Tue Mar 26 22:14:33 2002 +0000

    only sleep

Src/C_BaseLib/BLThread.cpp

commit 5a845b9c0b1e89d9f0499e170034e721f1f86277
Author: lijewski <lijewski>
Date:   Tue Mar 26 21:50:49 2002 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX
Tools/C_mk/Make.defs

commit 8e860ab2c2f086ee61e241fd2249a64efe75780a
Author: lijewski <lijewski>
Date:   Tue Mar 26 20:47:02 2002 +0000

    changes to work with xlC

Src/C_BaseLib/ParmParse.cpp

commit 41db2c66b7785026c28ffa0042eec720f37d69db
Author: lijewski <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 50d05247953df82ac63bb423da142cde578f2f01
Author: car <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 d64b94aa06f19b6d8048df2c7d7587f92d010bbf
Author: vince <vince>
Date:   Thu Mar 21 00:41:08 2002 +0000

    added -ieee flag for opal.

Tools/C_mk/Make.OSF1

commit 16a16c70b8ce2dedeaab9854a6513255139b37fc
Author: almgren <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 fda4fed36ab65026252e2dd2cfc759b33a7e1058
Author: almgren <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 e6be28de6ef81c5012d12876e94041fe61a982a8
Author: marc <marc>
Date:   Fri Mar 15 20:20:32 2002 +0000

    Rework frac calc to avoid using domain.numPts

Src/C_AMRLib/Amr.cpp

commit f4d29a5b96f3172c7160f9eb1abd5e1e6300b79c
Author: marc <marc>
Date:   Fri Mar 15 19:01:47 2002 +0000

    dsp maker for libs

Tools/C_scripts/dsp.lib.mak

commit 1a2aae2a35292283ee7aea3073b24d3ecf6e66d7
Author: car <car>
Date:   Thu Mar 14 23:56:07 2002 +0000

    fix for gcc3 and KCC

Tools/C_mk/Make.defs

commit 67a8b7f7a26f5016eab0df32a1d40d6f637dba7e
Author: car <car>
Date:   Thu Mar 14 23:05:16 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 7280f362b17135f87d0f1e67000324743caccb77
Author: vince <vince>
Date:   Thu Mar 14 01:48:58 2002 +0000

    changes for kcc 3.9

Tools/C_mk/Make.defs

commit 2f6b56e5e456c7309633886e2902802a0950b34d
Author: vince <vince>
Date:   Thu Mar 14 00:27:03 2002 +0000

    changes for brainerd.

Src/C_BaseLib/VisMF.cpp

commit 5706a47b53290026041fef7dcd8dc40c97928008
Author: almgren <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 9aeb3926cbf49d3f38339f54d859d6cf30b22438
Author: almgren <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 a2bd9985be187b7ef51d1f7940b0795a90d2ec33
Author: almgren <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 a12077709dc3cd9768693e427e1f6b0222f1b703
Author: almgren <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 e3da6dcb90d0f749c752aa74e81c3718490fbcb0
Author: almgren <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 35414c34a785792fc401ffb3fa5aeaeb7abbcea7
Author: vince <vince>
Date:   Wed Mar 13 21:43:58 2002 +0000

    Added FabArray shift for hchem support.

Src/C_BaseLib/FabArray.H

commit 2b6817e25de5e3fd3a8cff4b4e469642db7e06eb
Author: almgren <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 dd76577fcf71d6cd4dce02692c6736186c5aacdc
Author: almgren <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 128ba11362dc6ccdabf298925a329949cba32dfd
Author: almgren <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 e37fe41577d27773dddb077420f93186f98d3a83
Author: almgren <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 946f3bebd621cf4ea1d58cb65255c08fe0d78c2f
Author: almgren <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 7251e2539282c06ff2169ad638c700e6a3512e7a
Author: lijewski <lijewski>
Date:   Wed Mar 13 19:07:00 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/files.2d

commit 7ac1323ad3bc679a9eea15c479c9bacb47f4f3ad
Author: lijewski <lijewski>
Date:   Wed Mar 13 18:31:42 2002 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/files.2d

commit 557072c9b51a5fd38f0a66159585a12f031ed2e6
Author: almgren <almgren>
Date:   Wed Mar 13 18:29:38 2002 +0000

    Fixes for 2d only: length --> size, etc...

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 00c3ae75b9ef914f869f85ff40f06ea6fe418b2b
Author: almgren <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 32fb46a9fa29f66f14abb0d3702409ceaa09d942
Author: almgren <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 0be87707101752df7288f054d735d8b705ee2523
Author: almgren <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 b3d1c40d6b2053d77e5bfdb851d43556ce580c17
Author: almgren <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 fa0f4828fbda8b82198b4fab280e0ef83bef27a7
Author: lijewski <lijewski>
Date:   Mon Mar 11 23:05:53 2002 +0000

    added <cstdio>

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 1db1cf8f21bc862763e1e0aab5b1e2c304830e9b
Author: car <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 d19d40fe0409287d42896eadd5e8d68f25f2b800
Author: lijewski <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 c645c423c43c0edbc4c0afd991470473677dbd01
Author: car <car>
Date:   Tue Feb 26 23:41:45 2002 +0000

    gcc 3

Tools/C_mk/Make.defs

commit ac773995f938aa74a7f277f82f4d38ce7266b436
Author: car <car>
Date:   Tue Feb 26 23:41:31 2002 +0000

    some systems require explicit include of pthread

Src/C_BaseLib/BLThread.cpp

commit 773f7aee2cbb46af789391d1f1c6c1f1b243fd28
Author: car <car>
Date:   Mon Feb 25 20:59:43 2002 +0000

    UnitBox was implemented as a 2x2x2 box.

Src/C_BaseLib/Box.cpp

commit f0a852750a049c7a3fa2fd821633c0ef871635cd
Author: lijewski <lijewski>
Date:   Fri Feb 22 20:53:54 2002 +0000

    Fixed FixUpPyhsCorners() bug

Src/C_AMRLib/AmrLevel.cpp

commit 37c5c93cf3eea0d55cbf8513c70d6db7120116dd
Author: car <car>
Date:   Tue Feb 19 23:36:06 2002 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 65708e227dd6c8bb938aa11958d997cd5122412b
Author: car <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 40f18af7f515a218909d95552fb162b41d7f9bc3
Author: car <car>
Date:   Tue Jan 8 16:30:24 2002 +0000

    no message

Src/C_BaseLib/BLProfiler.cpp

commit 84ae1dc576e16216b9a0d4f091415a87d7f896e1
Author: car <car>
Date:   Fri Jan 4 00:17:23 2002 +0000

    no message

Src/C_BaseLib/BoxLib.dsp

commit 340126013477222f685556d51bdef3e19ab3ed74
Author: car <car>
Date:   Thu Dec 13 23:46:08 2001 +0000

    properly initialize m_used

Src/C_BaseLib/CArena.cpp

commit 0153c0121760b213e82d64987c997b7bd00b4b83
Author: car <car>
Date:   Thu Dec 13 18:24:59 2001 +0000

    makefile system knows fortran

Tools/C_mk/Make.defs

commit 943c3078102e14915169b8cd77532d1ac4b6c361
Author: car <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 7338c3102b9e9e68de937b5512c797459422f0a0
Author: lijewski <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 b8fffd2d095a50aa7765df1a0cc1faf7dc781a5c
Author: lijewski <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 f67ebf1d87578a29aa579c39bda572c39d28d316
Author: car <car>
Date:   Mon Nov 26 18:17:58 2001 +0000

    fix for max_threads

Src/C_BaseLib/BLThread.cpp

commit 72b1b8d357a72efdd80fd2b93f98bc3cce866557
Author: car <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 ebfe4014d13e0bbcec95aacabd448559863d2794
Author: car <car>
Date:   Wed Nov 21 19:50:44 2001 +0000

    CriticalSections seem to work better for mutex's

Src/C_BaseLib/BLThread.cpp

commit bc1964c02aed918d0cad48518a69298c924e2ca3
Author: car <car>
Date:   Mon Nov 19 19:10:49 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/BoxLib.dsp

commit 95489da9ba2256959f4ee197711f7ca5019f4ae0
Author: car <car>
Date:   Fri Nov 16 18:19:33 2001 +0000

    cv needs to be mutable

Src/C_BaseLib/WorkQueue.H

commit 87a79af96c58dd4833f0a614ed9341bc9d6005bf
Author: car <car>
Date:   Fri Nov 16 18:05:16 2001 +0000

    numthreads needs a lock

Src/C_BaseLib/BLWorkQueue.cpp

commit 1512164f13f9816fb51ddf730d9145f7b557ea77
Author: car <car>
Date:   Tue Nov 13 00:08:29 2001 +0000

    KCC doesn't always like PTHREAD_STACK_MIN?

Src/C_BaseLib/BLThread.cpp

commit 593758b9158c12f7ee1e39cfc41a1bfdc4459fee
Author: car <car>
Date:   Mon Nov 12 23:28:03 2001 +0000

    Windows fixes

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Utility.cpp

commit ed203ed26cab66b2073759a22901c804d7326c76
Author: lijewski <lijewski>
Date:   Mon Nov 12 21:38:21 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 0c2923f84cd4bfa17bafa3b79046dc34a5969beb
Author: car <car>
Date:   Fri Nov 9 14:33:10 2001 +0000

    fix for unix threads

Src/C_BaseLib/BLThread.cpp

commit 4fbf018518c7e3e45d0c89b9c83342141cd1d297
Author: car <car>
Date:   Wed Nov 7 22:00:57 2001 +0000

    More WIN32 support

Src/C_BaseLib/BLThread.cpp

commit 59ef849076489e3c12244f45809e14b4a78cf011
Author: lijewski <lijewski>
Date:   Wed Nov 7 19:05:01 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.AIX

commit 21c9b91122d3ca0d517904565273e7e847a5e579
Author: car <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 6ad4de3a6c65a0a15808dc7660d4247024ad5d61
Author: lijewski <lijewski>
Date:   Thu Nov 1 23:21:34 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 561b9d1587b491bef887ba1db57d66ba4abecc36
Author: car <car>
Date:   Thu Nov 1 18:53:15 2001 +0000

    baseThread

Src/C_BaseLib/BLThread.cpp

commit c232f425afcd75f8d08d1a167fed5200ccbfad7c
Author: car <car>
Date:   Thu Nov 1 18:46:37 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 66bd00cdca768fe158edea725612dc65455a83e9
Author: lijewski <lijewski>
Date:   Thu Nov 1 17:57:30 2001 +0000

    re-added BLMpi.cpp

Src/C_BaseLib/FabArray.H

commit b071e97be32c80a07c4968c95649614f7f970184
Author: car <car>
Date:   Thu Nov 1 17:08:41 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 3f6fd83617547211452bf2da1436c8dab7b69ec4
Author: lijewski <lijewski>
Date:   Thu Nov 1 16:50:38 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLMpi.cpp

commit 00bee9bc74ee65d750c9ef2b2c36d4889432a2ac
Author: lijewski <lijewski>
Date:   Wed Oct 31 22:42:01 2001 +0000

    re-added BLMpi.cpp

Src/C_BaseLib/Make.package

commit e627e541b531dc34fa913bdd7a11f048914d11b5
Author: lijewski <lijewski>
Date:   Tue Oct 30 22:03:42 2001 +0000

    more threading work

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit ed45f4779f07b8c1e3ab170b8e04d3f0d050cfe6
Author: lijewski <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 73776b926285e5ad8ad53d47eff3a2643dad0ed7
Author: car <car>
Date:   Wed Oct 24 19:48:44 2001 +0000

    PGI C++, which doesn't work

Tools/C_mk/Make.Linux

commit 3fa22817b73dcf71844375689ff83ae440590e36
Author: lijewski <lijewski>
Date:   Tue Oct 23 17:31:02 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit cd6a59b480c2872fecf1caa29708cf7c68fe4487
Author: lijewski <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 a4831f7b56e3a8422955c758e3255399c69a7d3a
Author: car <car>
Date:   Mon Oct 22 22:49:53 2001 +0000

    Fix for windows

Src/C_BaseLib/BLThread.cpp

commit 809eada7024f1a18ff23f9cba0302964326a2a93
Author: lijewski <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 f5889c9f31afe0c954987954f85507c228dc1d72
Author: car <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 c9909b4dd2a8063f7f8177ecf0da9454c31a4589
Author: car <car>
Date:   Thu Oct 18 21:54:13 2001 +0000

    Added BaseFab.cpp

Src/C_BaseLib/BoxLib.dsp

commit 5fccc81c64ee73f248f17fd4947af122596e4422
Author: lijewski <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 fefc4f87d6ef604efee3e8229b5ffa6a2e3c0d5c
Author: lijewski <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 e54230af302a6f45e042432a77ee54f2739dbbf4
Author: lijewski <lijewski>
Date:   Wed Oct 17 16:49:27 2001 +0000

    Need BL_USE_SETBUF for g++

Tools/C_mk/Make.defs

commit c94099a79dd5dd6abcdef11e5d3bbc8232e6e436
Author: lijewski <lijewski>
Date:   Wed Oct 17 16:43:22 2001 +0000

    always use pubsetbuf()

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit 2740e4dfcf09d12313d1ee2d58c647b440597abc
Author: lijewski <lijewski>
Date:   Tue Oct 16 22:45:34 2001 +0000

    got rid of libmiranda.a

Tools/C_mk/Make.AIX

commit e649e1df22dda44fa7f63ba342bcac5dd8dd0dc4
Author: lijewski <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 6ccd715d7d452b1067575222282b97aa5df438f8
Author: car <car>
Date:   Mon Oct 15 23:01:27 2001 +0000

    debugging flags for PGI

Tools/C_mk/Make.Linux

commit e404bf1f7116996057c874d0e1f640de99781256
Author: lijewski <lijewski>
Date:   Mon Oct 15 21:01:50 2001 +0000

    Set up PGI to use pgf90.

Tools/C_mk/Make.Linux

commit 53526c3e20db6da7d7dbcb6f05c4f1036ed6d98e
Author: car <car>
Date:   Mon Oct 15 18:37:35 2001 +0000

    Don't need the timespec declaration anymore.

Src/C_BaseLib/winstd.H

commit 511e100d285b3d3e0f9c1778703335039413ea04
Author: car <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 c4793ec6753d6f5105bc50ceb8d1c6b8889a29c1
Author: lijewski <lijewski>
Date:   Mon Oct 15 18:15:22 2001 +0000

    Removed COALESCE_FABS stuff and NEW_HFILES stuff.

Tools/C_mk/Make.AIX

commit a9e6bf828cc3d9049c463e700ed1625610343833
Author: lijewski <lijewski>
Date:   Fri Oct 12 17:44:25 2001 +0000

    added Mutex

Src/C_BaseLib/CArena.H
Src/C_BaseLib/CArena.cpp

commit 19508aeaeea6ff68492fde49d3ca0c5ca981d4a6
Author: lijewski <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 5abcc2bfef49ec67f5d53a6b68b4dd35382a7e30
Author: car <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 d0a6c086faef337326d9bcdbb4352d7b00c8e3ef
Author: car <car>
Date:   Wed Oct 10 15:44:41 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp

commit 54edbd0d50c809df8174036e6bb7a4fcc1632258
Author: car <car>
Date:   Tue Oct 9 22:37:46 2001 +0000

    MINGW32, a minimal gnu under win32

Src/C_BaseLib/winstd.H

commit 60eb4a06af049e53eb4b4a205e519ff036d72f60
Author: lijewski <lijewski>
Date:   Fri Oct 5 19:47:55 2001 +0000

    Up'd -bmaxdata size ...

Tools/C_mk/Make.AIX

commit d01fe1b5a1f083acaeb6afa7c6cfa8e4487ec93b
Author: marc <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 656bc02b52f7b929775c4f67a4b4d1731116f6b4
Author: lijewski <lijewski>
Date:   Wed Oct 3 19:53:51 2001 +0000

    output maxthreads only if verbose

Src/C_BaseLib/BLWorkQueue.cpp

commit 1537db3322396d3e8b4772420f03f71050206491
Author: lijewski <lijewski>
Date:   Tue Oct 2 16:30:41 2001 +0000

    mods to get working with KCC

Src/C_BaseLib/ParallelDescriptor.H

commit 4c926dce9a8f4a922acd0cce8a89dfe8a9d1aaad
Author: lijewski <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 505556fd4e49a16fe0fa8d9d66402098c49e71d3
Author: lijewski <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 aee10bdf4a73a569f0ade844dc6a60436dfdb0c1
Author: lijewski <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 40125ca78fd9409f89c22f8539d6a3941a016cac
Author: lijewski <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 8dccff2fa06f7e35617f621d2cac07aa73cc031c
Author: lijewski <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 4ea96634e2ed07b63c3a062900570254317a0e02
Author: car <car>
Date:   Thu Sep 27 16:11:49 2001 +0000

    -DBL_KCC_VERSION added

Tools/C_mk/Make.defs

commit c1d92c0d97a1f89f4b0db61fd8ca9fb67912c144
Author: lijewski <lijewski>
Date:   Wed Sep 26 16:59:53 2001 +0000

    removed unused variable

Src/C_AMRLib/FluxRegister.cpp

commit 94fa6304ba411508807038059c0e3581d702cfe7
Author: lijewski <lijewski>
Date:   Wed Sep 26 15:47:54 2001 +0000

     for clarity ...

Src/C_BaseLib/FabArray.cpp

commit a2ac2dbf22024f43d9499e0d4f2019cd08f9c641
Author: car <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 010f082397c359aa34b5e21d8458332c77faf825
Author: car <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 615a7e37f25fa5611280bf440deb8f6d13d2d04a
Author: lijewski <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 bc45a27eedb79b48cf1020fc42bf363f415417f7
Author: car <car>
Date:   Tue Sep 25 21:02:54 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit d14ad5bb55ba306d060ffc7e4b86ff1ab5d6f9aa
Author: lijewski <lijewski>
Date:   Mon Sep 24 20:31:35 2001 +0000

    output wallclock time since start(restart)

Src/C_AMRLib/Amr.cpp

commit 8c8b4b7973caa75e9e99829a49919a38454dfac2
Author: lijewski <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 2f0f0e61996e316968bd96cf94c4fa07965c84bb
Author: lijewski <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 60edfca6c7f74077055e505b3608b7295a154584
Author: car <car>
Date:   Wed Sep 19 17:04:43 2001 +0000

    no dependencies in real fortran

Tools/C_mk/Make.rules

commit 563494a2e228cfc5cf12bcb14b0c418156315b50
Author: car <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 952c4815d20dbb1d8ed588dd25c0ec1119b256be
Author: lijewski <lijewski>
Date:   Wed Sep 19 16:54:05 2001 +0000

    Added stuff to get threading to work.

Tools/C_mk/Make.AIX

commit d545ea4f211deb10f55d206a1d9fea9b0887e2af
Author: car <car>
Date:   Wed Sep 19 02:39:53 2001 +0000

    -CB loses mostly

Tools/C_mk/Make.Linux

commit 41b498cefb973fa40e6122d5657362cb4cc5ff89
Author: car <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 56f758554522df3a46fc6bddf2c73689dec87c95
Author: car <car>
Date:   Wed Sep 19 02:36:47 2001 +0000

    need header

Src/C_BaseLib/BLWorkQueue.cpp

commit 96738b65d66cee03e76e6b6f529398beab719dd6
Author: lijewski <lijewski>
Date:   Tue Sep 18 20:40:27 2001 +0000

    Wrapped an I/O statement appropriately.

Src/C_BaseLib/BLWorkQueue.cpp

commit 2be211fdda11abfdf72f98eebaf748a68c1c0c0f
Author: marc <marc>
Date:   Tue Sep 18 18:15:03 2001 +0000

    Split out tests for defined junk.

Src/C_BaseLib/std/limits

commit b6123d3def1832d49bafa18a0d1db887750cbf7f
Author: car <car>
Date:   Tue Sep 18 03:34:49 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 1af15535aed4c51625435aed2405108f0fb01c45
Author: lijewski <lijewski>
Date:   Mon Sep 17 22:03:03 2001 +0000

    add thread_safe for mpKCC

Tools/C_mk/Make.defs

commit 9f672695eb89ff0b03cc9a339ff8d92598f9f59f
Author: car <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 c0ec7a91985fce6cae6666710a76c2490c4d1b73
Author: marc <marc>
Date:   Sat Sep 15 05:29:29 2001 +0000

    Fix for little-f files

Tools/C_mk/Make.Linux

commit e11c4c3e107ec45f41a8e43344ee17eaf9955215
Author: lijewski <lijewski>
Date:   Fri Sep 14 21:03:06 2001 +0000

    Now always print out workqueue.maxthreads at startup ...

Src/C_BaseLib/BLWorkQueue.cpp

commit ad51eeaf15f9a17eab346f35aaa4c0f4f6608c77
Author: car <car>
Date:   Fri Sep 14 04:03:39 2001 +0000

    fixes for KCC

Src/C_BaseLib/Thread.H

commit 4ed862dda8fb12d8b5335357bd2629efbaa7dfb2
Author: lijewski <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 f9e972c082fc9e209dc823890cc0a8f9d847ba55
Author: lijewski <lijewski>
Date:   Fri Sep 7 23:06:44 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit 7ee4ea07b513769d4162ea38c473206bae7ce20e
Author: car <car>
Date:   Fri Sep 7 22:03:21 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp

commit 1571ac2fe7d8f61f5e950fb63fcaeab602c9c2a6
Author: car <car>
Date:   Fri Sep 7 00:35:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 7ffd979694028bb5cee2a5014d5e0451f4ec9236
Author: lijewski <lijewski>
Date:   Thu Sep 6 22:49:19 2001 +0000

    added a default getID() for USE_THREADS=TRUE.

Src/C_BaseLib/BLThread.cpp

commit bff607f2c7410026c398a34d92d4480f57a4b452
Author: car <car>
Date:   Wed Sep 5 19:29:59 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 7bf8fbdeb8ec8be84f216ea6c089e2463181735a
Author: car <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 cb249f2d02b38887bd56a58d0349cc0714bd082c
Author: car <car>
Date:   Thu Aug 23 21:58:04 2001 +0000

    simplify thread

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Thread.H

commit 74c37ccfc61562afb17833e40d84f9039d33f399
Author: car <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 d655e78ac0b422d598a5dad192a369f86dedafe8
Author: lijewski <lijewski>
Date:   Thu Aug 23 20:07:43 2001 +0000

    *** empty log message ***

Src/C_AMRLib/FluxRegister.cpp

commit 74f59b971996583ef9f4de210d6a25224903fb39
Author: lijewski <lijewski>
Date:   Wed Aug 22 21:35:25 2001 +0000

    removed an assert()

Src/C_AMRLib/AmrLevel.cpp

commit 6e907020406359bf8d19a1685358bee189082d32
Author: lijewski <lijewski>
Date:   Wed Aug 22 20:18:14 2001 +0000

    made probin_file default to probin

Src/C_AMRLib/Amr.cpp

commit 52b1c5d13a05df415d50bf33bec500113d61a70d
Author: lijewski <lijewski>
Date:   Wed Aug 22 19:21:00 2001 +0000

    reverted to older style copy constructor

Src/C_BaseLib/Geometry.cpp

commit 294a49a60fe976b3b65eac227d64991b8882e9ff
Author: car <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 d1464e70248a4cd6e37253ebd2c5cdea368c5e26
Author: car <car>
Date:   Tue Aug 21 20:30:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLThread.cpp
Src/C_BaseLib/Thread.H

commit 9d26ecb067c76786ed77c84309fa2116741d1eb7
Author: lijewski <lijewski>
Date:   Tue Aug 21 19:01:51 2001 +0000

    simplification

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 456a3ae0128e2e2b0b92ad22ed3b96847edfad93
Author: lijewski <lijewski>
Date:   Tue Aug 21 18:08:46 2001 +0000

    simplification

Src/C_BaseLib/FArrayBox.cpp

commit 2cbb6355ba144bb86384f0d09ee8f7464a0fac68
Author: car <car>
Date:   Tue Aug 21 17:10:31 2001 +0000

    minor leak

Src/C_BaseLib/BoxLib.cpp

commit db02b5832f404c7ba96390c719a8a44378d84498
Author: car <car>
Date:   Mon Aug 20 02:48:50 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit c9859153f8a77b678e659352afd0cb30d48b1d39
Author: car <car>
Date:   Sat Aug 18 23:39:10 2001 +0000

    added souce numega filters.

Src/C_BaseLib/.cvsignore

commit ae2120d7fa4996b5d70a9c643d4edd4687a90bfa
Author: lijewski <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 090cf8eca641b690acc31e6ec8c3f94ee254118b
Author: lijewski <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 6231b257f417a2d9a4cd61beda4fe9d9082b3549
Author: lijewski <lijewski>
Date:   Thu Aug 16 20:11:38 2001 +0000

    Refined the way we call ParmParse::Initialize().

Src/C_BaseLib/BoxLib.cpp

commit e41fa352b2e3ca5480f085af00c637bf437b7788
Author: lijewski <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 4fd2eb918db987631b802d06a74796c973591598
Author: almgren <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 eaf8a1067f7d656149f0debbd8de158ca9e4b4c7
Author: lijewski <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 070cf47016ace56ac0102995a86f78da961e3d15
Author: lijewski <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 e357e7c9b5a13b43c7bf0fcea54cb6255d50ea31
Author: lijewski <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 d1dfb90a598b4d2af7bbf9a4868eddb7ef661133
Author: car <car>
Date:   Tue Aug 14 22:14:00 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 91219641f2fbe46d4e8bbe1887d08e34e376b978
Author: car <car>
Date:   Tue Aug 14 16:07:31 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.dsp

commit 4b818a9c8be2dda01064db24595a4de795b91e27
Author: car <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 d924a7884add39a21663040dc725534262ef1978
Author: car <car>
Date:   Mon Aug 13 01:54:26 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 13f80b3c8c1dd6551a33dad7ac7d491aca831200
Author: car <car>
Date:   Sat Aug 11 21:19:04 2001 +0000

    MSVC fix

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit f1f03788ad06c84d2b8fcda1ae17a41ffd4c435f
Author: car <car>
Date:   Sat Aug 11 21:14:20 2001 +0000

    Fix for WIN32

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 4779d6475bc8d61d1f45ced82f48db7b3d95b633
Author: car <car>
Date:   Sat Aug 11 20:50:14 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 50a24751999bac22ccf18e2aa0c205a4bdc3d35c
Author: car <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 7ca19eb03d3bea063b85dc3ee0b9774458c0cb51
Author: almgren <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 168dac8e64af8e98ad65cf52f87b75a979be4759
Author: almgren <almgren>
Date:   Fri Aug 10 19:52:21 2001 +0000

    Changed the way we input periodic.

Src/C_BaseLib/Geometry.cpp

commit 3f31888d2bb5b9b2a02db3939ef3f7e90c46f200
Author: marc <marc>
Date:   Thu Aug 9 22:50:20 2001 +0000

    change fwd declare from class to struct

Src/C_BaseLib/Geometry.H

commit 2b555399f13bde8dd8b553150b97ebf1ca1a042c
Author: marc <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 7da8cbd5a8e1074c5030cefb5d6899a555b172dd
Author: marc <marc>
Date:   Thu Aug 9 16:21:26 2001 +0000

    Change concat function to satisfy DVF compiler

Src/C_BaseLib/REAL.H

commit 6246dcd469a073fafae66f452ad1563b3e7c86ca
Author: marc <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 8b4f114cca438e13c7488b8e6f813511999c33f6
Author: car <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 98053bd25277727478587fded0e5b6fc90e2eee2
Author: car <car>
Date:   Mon Aug 6 19:39:59 2001 +0000

    ParmParse hacks

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 7a200196d97ef17d0dec2912c234418cc00f4a3b
Author: car <car>
Date:   Mon Aug 6 19:39:25 2001 +0000

    windows

Src/C_BaseLib/VisMF.cpp

commit 4f5eb76456f5ffafb99dfd61df6d4af43ea7a653
Author: car <car>
Date:   Thu Aug 2 16:37:49 2001 +0000

    Typo

Src/C_BaseLib/CONSTANTS.H

commit 179787a5fcb97aee0a66f197b80b819b2f0422bc
Author: car <car>
Date:   Thu Aug 2 16:18:15 2001 +0000

    CONSTANTS change, use BL_REAL

Src/C_BaseLib/CONSTANTS.H

commit 13e54b2d1c1f686e482c8074db62fa16cf7da65c
Author: car <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 4861cf84a28a810339a8c2be7a7c4434332627ee
Author: car <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 0c2aef455851de50e4f28bd5d4da20c2544d2ce2
Author: car <car>
Date:   Thu Aug 2 01:23:44 2001 +0000

    BL_REAL macro to make constants

Src/C_BaseLib/REAL.H

commit 607c31bda376040fac7554f76f2f69d48c1a9533
Author: car <car>
Date:   Thu Aug 2 01:22:48 2001 +0000

    removed fwd decl of ConstFabArrayIterator

Src/C_BaseLib/FabArray.H

commit 50b636e221288017b1f4f1379d4a21e5ce6e8e80
Author: car <car>
Date:   Thu Aug 2 01:11:36 2001 +0000

    MSVC fixes

Src/C_BaseLib/Array.H
Src/C_BaseLib/FabArray.H

commit a6b5ed4084ee363bfb88fc0ade597cc4994b037c
Author: car <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 3ab16207380e889552c3db64b3849d86054faf41
Author: lijewski <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 5ee94906ecf8059e60fe6451b79cdeeee274beb5
Author: lijewski <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 36a19a67515e3a6483323827775c17bf460c4437
Author: lijewski <lijewski>
Date:   Wed Aug 1 18:14:13 2001 +0000

    now include <cmath> 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 e5a20cd0b01f1dc15fdc9ec74fb827e4fe67d3d7
Author: lijewski <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 6307a984e3a5f386a66ead7c89b38d01b1fa0e59
Author: lijewski <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 c070e2981e4189999c5442833935e8510d94d01d
Author: lijewski <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 b978fe82474e143ca4ce1ec7a641436c47b2bbdc
Author: lijewski <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 d541d3f7b9cac1eb84cd20c85213ad7482767877
Author: car <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 02bbcf0a2b49553e63fc3b8050bc00ac07e299e5
Author: car <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 66888f56bb1435e81e20f78b47094a6f8a95f8da
Author: car <car>
Date:   Thu Jul 26 20:27:27 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLWorkQueue.cpp

commit 610ec6d59f5d089366c4542245db84cd7f5192b0
Author: lijewski <lijewski>
Date:   Thu Jul 26 20:08:43 2001 +0000

    More forward declaration including <iosfwd>

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 fe0ade6dac7c302227c0f8dca448ced9c609996a
Author: lijewski <lijewski>
Date:   Thu Jul 26 14:55:25 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.cpp

commit de3b98c192c6a519f0dd9dda0d1f0956727a3097
Author: car <car>
Date:   Thu Jul 26 13:51:54 2001 +0000

    Removed redundant member

Src/C_BaseLib/FabArray.H

commit 28db7d5e9b348f876b3119dbd3fda41e4a5e3b35
Author: lijewski <lijewski>
Date:   Wed Jul 25 23:42:02 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H

commit a9f26ce1933ba28ed14b55b8bd5801441b22700e
Author: lijewski <lijewski>
Date:   Wed Jul 25 23:39:18 2001 +0000

    oops

Src/C_BaseLib/FabArray.H

commit cb1d70a6bb1881d4c58dd20ef8fbed4ce1a3726b
Author: lijewski <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 45acd51c22e4d75490c23853287efccf40a07a96
Author: car <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 e55d22dfe61e499614e94a95d4b4ffeed3631c81
Author: car <car>
Date:   Wed Jul 25 04:45:55 2001 +0000

    MFIter

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/MultiFab.cpp

commit 3132b853dd6e70f29b04264bc203a6f0175b6f63
Author: car <car>
Date:   Wed Jul 25 01:15:13 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit dd982e93bc711e72fc0d8f054948c8bbe3ec9222
Author: car <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 46f2c7ff7f39bea759610ba00225f720453fec32
Author: lijewski <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 4aafeaf6107718f38b66bdc7a4f7505e7f4c85e1
Author: lijewski <lijewski>
Date:   Tue Jul 24 20:15:38 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit 5be9e729ec5e8ce47dd7bc7656fa013fdd79e12c
Author: car <car>
Date:   Tue Jul 24 19:47:17 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit dd5db6e07b5e70ed390dd991bf5db2e5392dcb1c
Author: lijewski <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 f89eef51f99818d02eee1f4edd3a6606021779c6
Author: car <car>
Date:   Tue Jul 24 18:16:26 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BaseFab.H

commit 5bf0c158e55a5649574012b9f07ca0175acbd74a
Author: car <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 c59fef3681f7ad957123ca0e6af1d80e81ec032f
Author: car <car>
Date:   Tue Jul 24 14:38:21 2001 +0000

    removed 'options'

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 0bc94cd53a1aecc9ee77d95a92862f5d4e7dd471
Author: car <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 414b34c02cf7b42467d8f6a85cc024f6e779dfe3
Author: lijewski <lijewski>
Date:   Mon Jul 23 23:07:36 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxDomain.H
Src/C_BaseLib/BoxDomain.cpp

commit fc233189870228cff2e2d4d834fda3c8171edbc3
Author: car <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 7dbad4736377f38d1659343b3afdfc9f62abfd26
Author: car <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 8388d9bdf985c84b0a77afb5d2f5c772a3be5254
Author: car <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 214f85a0091a215508bcb4f8995c3b706a91f790
Author: lijewski <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 48bb8753c164fc17eaa1f991cf322f9608c24cef
Author: vince <vince>
Date:   Mon Jul 23 20:06:06 2001 +0000

    Added derived quantities.

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 07909795eaab050f4b542526317040d407f323d1
Author: lijewski <lijewski>
Date:   Mon Jul 23 19:34:23 2001 +0000

    *** empty log message ***

Src/C_BaseLib/WorkQueue.H

commit 0651a14b63b76d0d06be3aea87a0adbd40414eb0
Author: car <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 ddfa7c339a96f74bd0163562fc11fc80b9ece313
Author: lijewski <lijewski>
Date:   Mon Jul 23 18:15:21 2001 +0000

    aString is gone for good

Src/C_BaseLib/ParmParse.cpp

commit b7578effe6d5ebb9c15951a6e64fc16f3e6f78c1
Author: lijewski <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 1fd3e638cf5535f69ed85184557dfba1235adb59
Author: lijewski <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 76d21a521fb315769e65a08a07b53e0537396865
Author: car <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/pBoxLib_2.dsp
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 93d8e018a7dc489f25f23b36f81f422c44f14365
Author: car <car>
Date:   Mon Jul 23 04:25:47 2001 +0000

    *** empty log message ***

Src/C_BaseLib/test/.cvsignore
Tests/C_BaseLib/.cvsignore

commit 5f6ecb410104cbe0f90e9e2661e9db393a2a629f
Author: car <car>
Date:   Mon Jul 23 04:16:52 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp
Src/C_BaseLib/ParallelDescriptor.H

commit d8fb354c5578860044f86c39159ebca5e887e687
Author: car <car>
Date:   Sun Jul 22 23:46:40 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.cpp

commit db0180ceaa5ab6f6233e6264c0500c2b506fed86
Author: car <car>
Date:   Sun Jul 22 23:41:27 2001 +0000

    *** empty log message ***

Src/C_BaseLib/ParmParse.H
Src/C_BaseLib/ParmParse.cpp

commit 1a57891e2be31cae33c200263e17aea08d147bb2
Author: car <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 1b4363143dff469f4e0d03721eb526949c4cdf32
Author: car <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 da1cf99634256e3c24142c8a8a48ef53661dc73c
Author: car <car>
Date:   Sun Jul 22 22:12:10 2001 +0000

    Hides Profiling stuff in Initialize

Src/C_BaseLib/BoxLib.cpp

commit f786c7ec9fb5c9cda2f47cf69994a1818659a55f
Author: car <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 ab969a191c953ba0459d83b1962f4a02b9b870b0
Author: car <car>
Date:   Sun Jul 22 20:44:30 2001 +0000

    *** empty log message ***

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/Utility.cpp

commit df18db60a52d2fecf8dd2806fd0d412111b73cd4
Author: car <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 3a1cbcd2165138cd136dfde1eb40784eb65785f9
Author: car <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 c0e639ebc0bf85295111e10ea0eb4c7225593eec
Author: car <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 b4cf407b840b46a0160274912dd5b65463e07cfe
Author: car <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 8a0a69325b2062fd9c510a748edd5234b3fa4b27
Author: car <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 ceded93d6adac91197a69582f4fdf5be72b7b6d6
Author: car <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 263fd452085b6dda3cd605f54125d8b9060ecbdb
Author: car <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 2a9592e912a3c19c1d7bb0c9d77c1dfd83f53217
Author: car <car>
Date:   Sat Jul 21 17:37:09 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLProfiler.cpp

commit 3a22eedb143798978d9cce343267c73439e486f2
Author: car <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 6072d84b6ee1aa1d564552408c4cdec34cefa3d9
Author: car <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 e747b131a2c6e9760f2b9b34b3fdf006e4271c60
Author: car <car>
Date:   Sat Jul 21 00:33:15 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BLWorkQueue.cpp

commit 17cc3e4c642e156d30c8928f8e5e725d0ecad6b2
Author: car <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 9eb9fe061d135736d5a027b0988f4f618922ad1a
Author: car <car>
Date:   Sat Jul 21 00:32:37 2001 +0000

    *** empty log message ***

Src/C_BaseLib/WorkQueue.H

commit 4da74c2fc81d0a15f730210a9f005ee80eef4bc3
Author: lijewski <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 3e0fc393251268c16c2bfa81cff9fcf7b33b9cfe
Author: car <car>
Date:   Fri Jul 20 19:52:54 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxLib.H
Src/C_BaseLib/BoxLib.cpp

commit 119805bbd493a4855f33193ec6566b7fbfd3d0f0
Author: car <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 ee185be69acb0a96e0d5c95cf34c3163653a871c
Author: car <car>
Date:   Fri Jul 20 19:37:36 2001 +0000

    *** empty log message ***

Src/C_BaseLib/test/GNUmakefile
Src/C_BaseLib/test/GNUmakefile.test
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/GNUmakefile.test
Tests/C_BaseLib/tProfiler.cpp
Tests/C_BaseLib/tThread.cpp
Tests/C_BaseLib/tWorkQueue.cpp

commit bf5ac26094ad942aed1aff5c6d5e3f053c2ac4b9
Author: car <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 4cb4eb940846c55f088b9b0b029250f18a13d18d
Author: car <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 d0c4d1e7f611409b2130ba6069b36676b048f7e5
Author: car <car>
Date:   Fri Jul 20 17:57:27 2001 +0000

    Fixes for Parallel

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 00ec88d8a6d469dd2248bfed4c421b66eeff7d09
Author: lijewski <lijewski>
Date:   Fri Jul 20 17:28:16 2001 +0000

    Removed index>=0 checks ...

Src/C_BaseLib/aString.cpp

commit 458d2b7758915ecfe31f4e0c1c049207bcff8ed7
Author: car <car>
Date:   Fri Jul 20 17:24:30 2001 +0000

    windows normalization

Src/C_BaseLib/winstd.H

commit 8708f598def753a4c4c47750c25a430f3274fea8
Author: car <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 895fe410de54820a8113decdc08f0d167cd4be84
Author: car <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 d3dd6c8883c9d7f081db2aa5c63288f5d2b04065
Author: lijewski <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 492b2dd33dbc132cf2e580ed3ee08e8e4d115f4a
Author: car <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 541ab33dc1f2c68c40741c5cb1120ef296077723
Author: car <car>
Date:   Fri Jul 20 01:45:48 2001 +0000

    *** empty log message ***

Src/C_BaseLib/Array.H
Src/C_BaseLib/PArray.H

commit db544835aae20e557145739964c8fd4b065b5b03
Author: lijewski <lijewski>
Date:   Thu Jul 19 21:31:09 2001 +0000

    Fixed a small bug we introduced.

Src/C_BaseLib/IntVect.cpp

commit 0a3ddc2c777b072569bbae9a10f356c5abdc5db1
Author: lijewski <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 2eb7c3648c7873fe5428a440e3ecb9523a54a274
Author: lijewski <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 144474b170bf410f7db37edd373758a89bcdef21
Author: lijewski <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 2444fec9e4f13656da3bc852469661c2074f68af
Author: lijewski <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 a42750a4f63bf9f1391c22a7f2a28272b032cd12
Author: car <car>
Date:   Thu Jul 19 17:19:33 2001 +0000

    *** empty log message ***

Src/C_BaseLib/BoxList.cpp

commit fe6d382d47a6b657ed2d7089d5111da4359de195
Author: car <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 a09146b8a8d5240ebfb5f7721e6b504178136702
Author: lijewski <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 04dc038efd1583da3cc53d6c6f499ec5eb20404f
Author: car <car>
Date:   Thu Jul 19 16:51:22 2001 +0000

    *** empty log message ***

Src/C_BaseLib/IntVect.H
Src/C_BaseLib/IntVect.cpp

commit c25819a54c677da47d0c12ac295bbd196d393596
Author: lijewski <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 7b07ed5fd5bbb0ec00d96b207beb080b36da31f8
Author: lijewski <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 a5ae665e58d0066e544d7108630538e88e49b8df
Author: car <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 c08d75c01dd3c9619320fa19301c67fe72c70707
Author: car <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 07096d004bd7634eae125585c7130e9e080e9cd2
Author: car <car>
Date:   Wed Jul 18 20:41:04 2001 +0000

    Max->std::max

Src/C_BaseLib/MultiFab.cpp

commit 0fdbdc32420aeb09ba4a5763480fa055393b704c
Author: car <car>
Date:   Wed Jul 18 20:40:29 2001 +0000

    Abs->std::abs

Src/C_BaseLib/NormedFab.H

commit ece515b8b90c8b6d88b87338b0ca906fcc591f8c
Author: lijewski <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 960998ddc9854bb8808455e236877e348c59e268
Author: car <car>
Date:   Wed Jul 18 17:33:04 2001 +0000

    another Max

Src/C_BaseLib/RunStats.cpp

commit 3dda2c5f913b99365660b22883af83dd2bfb16b7
Author: lijewski <lijewski>
Date:   Wed Jul 18 17:31:06 2001 +0000

    2-D bug

Src/C_BaseLib/FArrayBox.H

commit 9ac5650570454de8b4c6ff84714dbfb2030cff65
Author: car <car>
Date:   Wed Jul 18 16:46:09 2001 +0000

    fix for KCC 4.0f

Tools/C_mk/Make.defs

commit 4b9dcba225837ec76148a5f35ae0bc093ff7fb66
Author: car <car>
Date:   Tue Jul 17 23:40:08 2001 +0000

    Fortran process // comments

Src/C_BaseLib/CONSTANTS.H

commit 49dabc84220dae228faa94be94e23a55fb1d214a
Author: car <car>
Date:   Tue Jul 17 23:14:38 2001 +0000

    Fortran can't process // comments

Src/C_BaseLib/REAL.H

commit d2b02bb9fd9a4e68cdc11e39ecd7749d775c0e15
Author: car <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 ebc4348b0ea25c18de05280b3b5c8f46264085e4
Author: lijewski <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 20ea450d5bacb94a138f4e68d4f2f994eb3e7a22
Author: marc <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 d26c95901637953609e9658acf3fee0b4a05a8f4
Author: lijewski <lijewski>
Date:   Tue Jul 17 16:58:05 2001 +0000

    Added for GNU

Src/C_BaseLib/std/limits

commit 9cf1b03da1783de2f245ce6765cf646cb90e0364
Author: lijewski <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 8c57c289f5f0a571e29b688b274ba8a37c887db4
Author: car <car>
Date:   Fri May 18 16:49:24 2001 +0000

    ampersand is a better continuation character, RE:
    Fortran standard

Tools/C_scripts/strip72

commit 45bf7856a1b4e60f65a06cba1bacfeec09545941
Author: car <car>
Date:   Thu May 17 21:52:13 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 2f33619f91dbbb8edd38dbcae15165cc9b4bc49e
Author: car <car>
Date:   Tue May 15 16:31:23 2001 +0000

    changes in flags

Tools/C_mk/Make.Linux

commit 474211cbed5e054dcc83dbdd3443e6e66b9ceecf
Author: lijewski <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 accac0edbdde7da47aee66bffcfc435c7c720bf8
Author: wyc <wyc>
Date:   Fri May 11 19:44:24 2001 +0000

    added small change to handle PGI compiler

Tools/C_mk/Make.Linux

commit 5c051fdab3e7f9fb3fc761333ca5bd6c0aecbd33
Author: lijewski <lijewski>
Date:   Thu May 10 17:16:40 2001 +0000

    No longer compile in Tracer.[H,cpp]

Src/C_BaseLib/Make.package

commit 06d98cedc903b8906128c4e9ba3610b334f1fc9c
Author: lijewski <lijewski>
Date:   Wed May 9 22:42:22 2001 +0000

    Simplified report().

Src/C_BaseLib/RunStats.cpp

commit f752ef017bc6bcd6eab57be6cd0280934da94d7b
Author: lijewski <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 9f82b3a331ea3dd3276717c7bd9cf159190a5bdd
Author: lijewski <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 d25966fbbb681b52756b28963a254b756b65366c
Author: lijewski <lijewski>
Date:   Wed May 2 20:20:40 2001 +0000

    New -L option for mpi on OSF1

Tools/C_mk/Make.mpi

commit 59f48531524902d4f1b70524255c0e57dd9d2e74
Author: car <car>
Date:   Fri Apr 27 20:07:11 2001 +0000

    Added support for Intel compiler

Tools/C_mk/Make.Linux

commit d095581fc3a671b6e671dd984526c7dcfd57c3f8
Author: car <car>
Date:   Wed Apr 25 22:54:09 2001 +0000

    minor bugs

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 4e37cdf11f1299a1240cbc9109834890713f9d7c
Author: car <car>
Date:   Wed Apr 25 04:16:20 2001 +0000

    isDouble should return bool

Src/C_BaseLib/ParmParse.H

commit 4320997c40c7a076bfa26ad151f982f439c21add
Author: car <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 05a794911c8fa1895116458712f4ad2110a9f0e1
Author: car <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 54915ae813efe0e899252b662a7cba8317cfb610
Author: car <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 5c56faf642d0ecf9f1c0edb53a3859a7bf714a7f
Author: car <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 9a76ca7865c972547e473676673f7fdcd98960e0
Author: lijewski <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 69c03f399e9669a8b531e586b595f3c254d949fb
Author: car <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 442b07a5ef7ad2834ab366f5d055a6b12aa5a7ee
Author: car <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 4e814f50a627ee16f5a785f3c048568fceab53a8
Author: car <car>
Date:   Mon Apr 16 21:32:55 2001 +0000

    *** empty log message ***

Tools/C_util/wrappergen/wrappergen.c

commit 7726a96ae89ed840e28abffae41bbe190b8a1d9f
Author: car <car>
Date:   Fri Apr 13 17:18:54 2001 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit 2c3a61dc1989b2dcb8b9ed74559fcdb38f3b8f38
Author: lijewski <lijewski>
Date:   Wed Apr 11 18:11:04 2001 +0000

    Further simplification to copy().

Src/C_BaseLib/FabArray.H

commit cc6a1f5887637dbe83a1c9a0daf679ca9249293a
Author: car <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 9e44d7658f6a6e6098828077bb0f26e00e8800d3
Author: car <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 7788fa29ae4a64a331133d5092781237f27a3911
Author: car <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 b80511fe127a3c79c71da7e7d12686e058de3366
Author: car <car>
Date:   Fri Apr 6 20:04:52 2001 +0000

    MPI off fix

Src/C_BaseLib/VisMF.cpp

commit b889ecda54866c6f6062cce4e7060225c44f0773
Author: lijewski <lijewski>
Date:   Mon Apr 2 17:58:59 2001 +0000

    Now use MPI_Waitsome() instead of MPI_Wait() ...

Src/C_AMRLib/FluxRegister.cpp

commit c523a2c3c5fcfded4ac2212dccfed152f83e6c0d
Author: lijewski <lijewski>
Date:   Mon Apr 2 16:48:31 2001 +0000

    Simplified and improved the MPI stuff ...

Src/C_BaseLib/VisMF.cpp

commit 6df19fad2e2e9f85aa7781a75b57d84a7bc426d0
Author: lijewski <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 062f2ed0748bb776dd8715c3713b91c2cafffec2
Author: car <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 69bff66267c8546b9ef2bc6d90d5693138a98aa9
Author: car <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 7af1766c271cca624ff4a650fcc649948e3d2513
Author: car <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 270f0d6b65534d0a66bad85c8ec225b4b880b7eb
Author: car <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 02efa9186a7f2661fcb53dd5903319782aae95e7
Author: lijewski <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 38b7ae9e1ef0be4596eb58ad3df33e481ea8445a
Author: lijewski <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 83820460d16364bb879e7404133faf832fb20cb3
Author: lijewski <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 1d54376658eec160d74835f87556eca9d9ff3358
Author: car <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 58d6cd81f2614532fd7121723481db1c77cadf5a
Author: car <car>
Date:   Tue Mar 20 19:42:02 2001 +0000

    maxorder flag

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 9e7d560f5940144e8ce863e335ec40ff932600a8
Author: car <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 f7ec482f6e979fb2ad975af96bac4e51ec14d6b8
Author: car <car>
Date:   Tue Mar 20 19:40:43 2001 +0000

    namespace correction

Src/C_BaseLib/ParallelDescriptor.cpp

commit f98dd1d369a6d4b9c4e5771f346fe736da268400
Author: lijewski <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 9ce53ef9b3f9dbd8acec52ec7bdeb6f154b832ac
Author: wyc <wyc>
Date:   Thu Mar 1 21:17:34 2001 +0000

    added preprocessor foobah to protect squirrelly namespace stuff

Src/C_BaseLib/ParallelDescriptor.cpp

commit fe4623ab58a814823b7a0502a68608cc0d8abc74
Author: lijewski <lijewski>
Date:   Wed Feb 28 18:07:31 2001 +0000

    Removed FORT_FLUSH stuff ...

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit 26590854a8d32d17ab97f8c4f315be2ea071ef29
Author: lijewski <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 9c2fecb29d3bfc25899f0b6114e93d929f498d98
Author: marc <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 e87c37ea4d565279be53c6909d4e83cae7af2694
Author: almgren <almgren>
Date:   Fri Feb 16 22:59:51 2001 +0000

    Don't need this declaration.

Src/C_BaseLib/COORDSYS_2D.F

commit 79a7e89ed9167d48a6313d3e26baf75e935b0afd
Author: lijewski <lijewski>
Date:   Wed Feb 14 19:05:44 2001 +0000

    Deprecated BL_USE_ARLIM junk

Src/C_BaseLib/ArrayLim.H

commit 608b37605fcf53f34c94f2a0514e9179f91faf22
Author: lijewski <lijewski>
Date:   Wed Feb 14 17:57:57 2001 +0000

    Deprecated BL_USE_ARLIM ...

Src/C_BaseLib/ArrayLim.H

commit 4cbe6b88621882c0e5d46b933a4686557c36c4f3
Author: lijewski <lijewski>
Date:   Thu Feb 1 23:39:35 2001 +0000

    Removed AlternateApplyBC junk.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 9497fe6569d65936ff8791b0c839626f5cc9cb43
Author: lijewski <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 2f9df0984b5181857887781cfe7736bf45040643
Author: vince <vince>
Date:   Thu Feb 1 21:28:27 2001 +0000

    Added support for cygwin under nt.

Tools/C_mk/Make.CYGWIN_NT

commit 91e4cef93536c11dfe595e021ed8e942e8d1a06a
Author: vince <vince>
Date:   Thu Feb 1 00:49:02 2001 +0000

    Added support for cygwin.

Tools/C_mk/Make.defs

commit 915c11625d2e44d074a9e873d3ec35e933f86635
Author: lijewski <lijewski>
Date:   Fri Jan 26 18:08:14 2001 +0000

    Forgot the non-MPI section

Src/C_BaseLib/ParallelDescriptor.cpp

commit 615cc7c8ea2317260c103d425341bb51cd762c11
Author: lijewski <lijewski>
Date:   Thu Jan 25 23:53:23 2001 +0000

    Removed a BL_ASSERT() ...

Src/C_BoundaryLib/FabSet.cpp

commit 554df82eef286c07119bb52721e389e982ca7a90
Author: lijewski <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 2319790954670e34791848da20227528bf935bb3
Author: lijewski <lijewski>
Date:   Wed Jan 24 22:50:47 2001 +0000

    Now compiles.

Src/C_BaseLib/test/tCArena.cpp
Tests/C_BaseLib/tCArena.cpp

commit 8f4ee998bc991029d3650a27e71ff07cfc884893
Author: marc <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 cd402d553859c9b47281a06d5124d1ab0b4405c0
Merge: 6af1b99 f4b1e81
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jan 4 06:52:45 2001 -0800

    Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib

commit 6af1b9924a9b1228b0ec2422c6f58198faa18b43
Author: Matthew Emmett <mwemmett@lbl.gov>
Date:   Thu Jan 4 06:51:17 2001 -0800

    PyBoxLib: Fix int size bug.

Src/Python/F90/fboxlib/boxarray.py

commit 53877e03c2fbb19d05c69f228c4d44f9d1551750
Author: Matthew Emmett <mwemmett@lbl.gov>
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 c73895bf0473f31d438fbf61e3b1a8eab0d2aef6
Author: marc <marc>
Date:   Thu Jan 4 00:49:52 2001 +0000

    Fix up script a little more...

Tools/C_scripts/dsp.mak

commit 7bf13ad9d41cd15de8f4db03761d88edf4f08c07
Author: car <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 cd05d23c7e5844d1658a741eb1c564a4d3d973c9
Author: marc <marc>
Date:   Thu Dec 7 17:39:05 2000 +0000

    Small mod to script for opt

Tools/C_scripts/dsp.mak

commit 4210273ac49aeda78a87652f51810ec693bb023c
Author: marc <marc>
Date:   Wed Dec 6 23:44:28 2000 +0000

    Set maxmem stuff to be unlimited

Tools/C_mk/Make.AIX

commit 0c16ad5499e6279f098aa67279be67604664dd3d
Author: almgren <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 654f0af7157028ab18bf91f31c250874903f7b3a
Author: marc <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 717d426583d34f9fa468fb7415a6b97d31aec4d3
Author: marc <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 d5055592ae171fad801b9cd6c168aab11f3db290
Author: lijewski <lijewski>
Date:   Fri Nov 17 18:01:09 2000 +0000

    Consolidated some duplicated code.

Src/C_AMRLib/StateData.cpp

commit 2ce475ab450077b2f7bf27113d4ca2668d0f4c13
Author: lijewski <lijewski>
Date:   Fri Nov 17 18:00:55 2000 +0000

    Little simplification ...

Src/C_AMRLib/Interpolater.cpp

commit 4a23d6ba0d3f64303e446eb1dfbf7e8fbce2b680
Author: car <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 a177b8a4b8df9c42b57ec49ec148db337edc4e91
Author: car <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 ad65d4ca7dc1e208eadecc5c6a314c4c30920312
Author: car <car>
Date:   Wed Nov 8 22:01:50 2000 +0000

    book != bool

Src/C_BaseLib/BaseFab.H

commit 372e4f3d2953477cc8fa7823d854bf73be7e7161
Author: lijewski <lijewski>
Date:   Wed Nov 8 21:48:21 2000 +0000

    Added bool isAllocated () ...

Src/C_BaseLib/BaseFab.H

commit 5d258cebfdcfcfd5c09ebfe376340cdd7f3ff1bc
Author: lijewski <lijewski>
Date:   Thu Nov 2 23:07:27 2000 +0000

    A tad simplification ...

Src/LinearSolvers/C_TensorMG/DivVis.cpp

commit 19ef426a2df4d45548331254f71a807606b32b74
Author: lijewski <lijewski>
Date:   Wed Nov 1 18:29:37 2000 +0000

    A little simplification ...

Src/C_BaseLib/CoordSys.cpp
Src/C_BaseLib/RealBox.cpp

commit 777012a28e662cc6369c56b682d8fa9f67de6f53
Author: lijewski <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 95bde516e944c08ea75648116dde5cd64244c6cf
Author: lijewski <lijewski>
Date:   Tue Oct 31 21:11:21 2000 +0000

    Minimized memory overhead in MF -> FAB copy().

Src/C_BaseLib/FabArray.H

commit ae8bf669721a0ddce9c64c8d20943307eed7d89b
Author: vince <vince>
Date:   Fri Oct 27 00:50:18 2000 +0000

    Added setbuf ifdefs.

Src/C_AMRLib/Amr.cpp
Src/C_BaseLib/VisMF.cpp

commit f22ac494841ca056006d8083577d231b429fe2d5
Author: lijewski <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 67f4fa93693fd6ad37ecccbdc5b3dc2cca3f3792
Author: lijewski <lijewski>
Date:   Tue Oct 3 20:26:49 2000 +0000

    Small change for BL_AIX

Src/C_BaseLib/Utility.cpp

commit 39eb97cda4f5388271cb3e2e6d1ca890ae30bdb9
Author: lijewski <lijewski>
Date:   Tue Oct 3 18:17:27 2000 +0000

    Added an explicit type

Src/LinearSolvers/C_CellMG/LP_2D.F

commit 3a9d361ae57314f5fd0f6dce7e4a42c3fbdaae7f
Author: lijewski <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 ddf16584419bc094589265a5b5005a8c3e8b7067
Author: lijewski <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/Banner.html
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 4f44d49e2b0ca282d570a9f3ac6e1b8a1400773e
Author: car <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 deac8f533e93d01229c236aef5aae5cfb4809a54
Author: car <car>
Date:   Tue Sep 26 18:19:25 2000 +0000

    helper macro for FORTRAN calls

Src/C_BaseLib/ArrayLim.H

commit a4f4bb39e485eba0d0b395e771627bcce55d7725
Author: car <car>
Date:   Tue Sep 26 18:18:57 2000 +0000

    fix for min max

Src/C_BaseLib/MultiFab.cpp

commit 4871a2a2a7650117374f1ccdee11a8ba51c732ac
Author: almgren <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 cfc4838f0feef303f9784ff0f0f5a79fa4d03ab1
Author: lijewski <lijewski>
Date:   Thu Sep 14 15:25:26 2000 +0000

    Cut down on sleep time.

Tools/C_scripts/compressor

commit f90bf5d33476ce0b7ad156a8053bb7f973c8eca3
Author: lijewski <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 74def7afe2743f35c1f9e04b45ca5755a5509794
Author: almgren <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 c3e40459c4fea2aab32bd6fd7ea2f43c7413c646
Author: car <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 b3c233c679d93ff3de07fd7114de63e8aa2c6050
Author: car <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 bbfe3a7fe6b93ca4ed297ace0ea583a6e67a6748
Author: car <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 e18930dd8980331b3db00b8da636f31d39646f73
Author: car <car>
Date:   Sat Aug 26 19:41:00 2000 +0000

    3D Norm

Src/LinearSolvers/C_CellMG/ABec_3D.F

commit 1005091f9b69669c6118bc91b239c146710c6c30
Author: car <car>
Date:   Fri Aug 25 19:23:28 2000 +0000

    fix for bicg with initial zero residual

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 8027c545e31dca56d82c4cb7b783d53568e1be81
Author: car <car>
Date:   Fri Aug 25 17:50:25 2000 +0000

    annotation tweak

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit 48f5dd911040a2300a34e25aa432ed4ffb233e18
Author: car <car>
Date:   Thu Aug 24 22:45:46 2000 +0000

    profiling fix

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit b1396521f4c307c983ef96f9137ab09a0aaa7af1
Author: car <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 e9cc8cc18dc55469731909f6a21c863603c6051c
Author: car <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 dda17304a1fd7d40ab3120d1875fa011a857cf45
Author: car <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 8250cc7d59aef20787e938ce45dc2ad914b0bec2
Author: lijewski <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 ef2f6f0408b5ce50fe1b440ee4ec430205c27464
Author: marc <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 a19ba918b0818a1b0a60bc2c06a6be6fe8a83b8b
Author: car <car>
Date:   Tue Aug 15 19:37:31 2000 +0000

    Make.mpi

Tools/C_mk/Make.Linux
Tools/C_mk/Make.mpi

commit 432774dcee5c7ff38d3427a6bde14eb513e263ef
Author: car <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 579223d7042855d17fa0d5de0284567ccf601276
Author: lijewski <lijewski>
Date:   Wed Aug 9 20:23:04 2000 +0000

    Removed an unnecessary parallel reduction.

Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp

commit 3eb3ab21e37f06866e6bf48d1e3738e446547239
Author: lijewski <lijewski>
Date:   Wed Aug 9 15:38:50 2000 +0000

    Removed unnecessary paralllel reduction.

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 3021b995053a410a82f28944c1b6622450002d25
Author: car <car>
Date:   Fri Aug 4 18:06:22 2000 +0000

    another Profile

Src/C_BaseLib/FabArray.H

commit 87f0536024bc437703a24c8d8861204209130a69
Author: lijewski <lijewski>
Date:   Fri Aug 4 18:00:58 2000 +0000

    Removed need for MPI_Gather() in copy().

Src/C_BaseLib/FabArray.H

commit a19a101d3af0f85b1dd81611b860f5251471090d
Author: car <car>
Date:   Thu Aug 3 18:27:51 2000 +0000

    c++ comments in fortran

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F

commit 452223627bb3c27ae6aa92d665c00b19edf70213
Author: almgren <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 25ef08c29e0cae8258bdcbb465aa4f1ea983527c
Author: car <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 b086769b7d0b120b8cec9d0c200b780b8a2c59a3
Author: car <car>
Date:   Wed Aug 2 16:09:45 2000 +0000

    MPICH 1.2.0 Support

Tools/C_mk/Make.mpi

commit 20cfbc5f4114692f0b3504f53281d5fa4f07f0dd
Author: car <car>
Date:   Wed Aug 2 16:08:35 2000 +0000

    Thread Safety Support

Tools/C_mk/Make.defs

commit 25a81c68d12d649896e8704c2913d5854c02a1e9
Author: car <car>
Date:   Wed Aug 2 16:08:10 2000 +0000

    profiling support

Tools/C_mk/Make.Linux

commit 121e11bcb567a312a97cf6fe4b54baea89db40d4
Author: car <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 297b4da4482ff10708962eb582ed69bc49da1eef
Author: car <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 f80d6376d625c79fc0a8c1c5080dd4d471bcf9de
Author: lijewski <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 a6e43c29167e907b36fa2ac9c9655981e2840a33
Author: almgren <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 ea8150399aa431d51be7c59d41c0ce4615e09441
Author: lijewski <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 e956870b64038e4b18bf763a8029198316756d05
Author: lijewski <lijewski>
Date:   Wed Jul 19 19:53:36 2000 +0000

    Removed some unused foo ...

Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F

commit d8a57f1d471e18b03d0748ea3eece60467c4befa
Author: sstanley <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 3ab7f11361dd8f47e80b370147e696baedd90b6e
Author: sstanley <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 7f327cf5c92acf28ab3fcb3d08f1755a79134985
Author: sstanley <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 74cd882b7180e0d53bc039c0c0544e7833f547de
Author: sstanley <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 f0001fb78404ff86eea427264c9fc7fbe919d94c
Author: sstanley <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 0ed5d98be98015e2a5c3e4cc091a2d8f7a32dc2b
Author: almgren <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 a3f09374c9c2b25fdb68bf244f3b304b101b51fc
Author: almgren <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 6b1030d94e93ed9c9d0b8118031ad84cb4b09c33
Author: sstanley <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 00fc8257113ec51d5675ff5a582fa10b85fc30f9
Author: sstanley <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 08e0f189222c3769fa06630243455bdc02def5af
Author: lijewski <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 7a82ebf8289d5f16ea4a059384c57779ada2d208
Author: lijewski <lijewski>
Date:   Thu Jul 6 17:03:57 2000 +0000

    Protected a couple cout's with IOProcessor() checks.

Src/C_BaseLib/ParmParse.cpp

commit b594acc0386a1d8dfee1569152309b5cb6d4a23f
Author: lijewski <lijewski>
Date:   Mon Jul 3 23:40:02 2000 +0000

    Tad more simplification ...

Tools/C_scripts/compressor

commit 971f20a69172962eb6f62eaad21e827fd7ed9f83
Author: lijewski <lijewski>
Date:   Mon Jul 3 22:02:50 2000 +0000

    Removed couple declarations that were never defined.

Src/C_AMRLib/FluxRegister.H

commit ef6fc9193d89d5bd67a5d54987ceb433caf57218
Author: sstanley <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 63f303256f22d9f1a2a37103c1324793c78b317c
Author: lijewski <lijewski>
Date:   Tue Jun 27 20:54:50 2000 +0000

    Removed "inline" from isBoolean() definition.

Src/C_BaseLib/ParmParse.cpp

commit e8e18cc1d0d6fb24896df0f3aa3aee160319d420
Author: lijewski <lijewski>
Date:   Fri Jun 23 16:48:00 2000 +0000

    Uped maxmem for optimization a tad more.

Tools/C_mk/Make.AIX

commit d3920901615641d037f29e3972d699f20dde3dcd
Author: car <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 5b03ac68d65808c3028cd523427898a86faf583c
Author: car <car>
Date:   Thu Jun 22 20:56:22 2000 +0000

    ABecLaplacian.cpp

Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp

commit 42cdda2aae628627a99cce611624c34eb7a693f1
Author: car <car>
Date:   Thu Jun 22 20:00:15 2000 +0000

    Threading...

Src/LinearSolvers/C_CellMG/Test/GNUmakefile
Tests/LinearSolvers/C_CellMG/GNUmakefile

commit 70a8e9ba198fc1cb3b0c16ef334707e66a7c9174
Author: car <car>
Date:   Thu Jun 22 18:34:50 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 11204ec79c2f39258ba1664fcbb9524409b6f0a8
Author: car <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 a9553f052da123848f68617f923424e488e25cab
Author: lijewski <lijewski>
Date:   Thu Jun 22 16:07:32 2000 +0000

    ::intersect() of two BoxLists wasn't right.

Src/C_BaseLib/BoxList.cpp

commit a579f62055cc70010c1b30162ea5fe9e47bb8a17
Author: sstanley <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 3b224ab5ea2991fe681551e16b1bf0e02484587e
Author: sstanley <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 cc939879d10f359d34888192af7245c59c8d1d00
Author: sstanley <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 6531cefa05f58f8c92a3d4c4486fcacb973854e4
Author: marc <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 a34738e916bc793eaa0b07c15eadc369b78bd36d
Author: lijewski <lijewski>
Date:   Tue Jun 20 21:44:11 2000 +0000

    A little more finagling with sleeps.

Tools/C_scripts/compressor

commit f53524a86239e12f1e8cb769b51d4d9b2da44800
Author: lijewski <lijewski>
Date:   Tue Jun 20 20:45:51 2000 +0000

    Changed sleep interval.

Tools/C_scripts/compressor

commit 3a347c6156dd367e7d64f4d879a4ed64b3ecd7d6
Author: lijewski <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 8574964f67dc368e8e99341dcd70184c06ed2f17
Author: lijewski <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 eed44d5efc8638f4eab151bbfe5cb93c44bfbf4c
Author: lijewski <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 17046cc985d854838fb1583f56b77d7c2b736c42
Author: lijewski <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 317f2e0f37dcb96ab6dc717a1469673f1a99e169
Author: almgren <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 26725162ae72c0a69b58a4ad9edaf70be78825dc
Author: sstanley <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 de276e2b8688d319a9038624f3b36058b0f4afa2
Author: lijewski <lijewski>
Date:   Fri Jun 9 21:10:31 2000 +0000

    Use CXXFLAGS instead of XTRADEFS in one case.

Tools/C_mk/Make.AIX

commit 4b31e60de2c5f613f19d2ff19e945ce20bfa6ccb
Author: sstanley <sstanley>
Date:   Thu Jun 8 20:26:33 2000 +0000

    Added a few constants that I needed.

Src/C_BaseLib/CONSTANTS.H

commit b0b8fd61ce0378193741b1bdf0b921b7ab996fbf
Author: lijewski <lijewski>
Date:   Thu Jun 8 17:38:02 2000 +0000

    Increased maxmem a tad more.

Tools/C_mk/Make.AIX

commit 8bf76dd598f730dc086606d3a2e2f5ac21640a80
Author: marc <marc>
Date:   Wed Jun 7 23:18:11 2000 +0000

    Reverse order of define and namespace close

Src/C_BaseLib/Specialize.cpp

commit b1427779324bf91a52e9179f87e56e6799cb09b9
Author: lijewski <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 881da75d136ad28ae4ea8e555f514a5311d27ed8
Author: sstanley <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 a1f4a27a10585a5b94e88911e95d01dca1d1475b
Author: lijewski <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 b5dbd69d4769dc9d1a3f7c9b2d2be405de73c510
Author: car <car>
Date:   Mon Jun 5 19:11:16 2000 +0000

    namespace fix

Src/C_BaseLib/ParallelDescriptor.cpp

commit 3331e600a69c44a664d861da3d12222ad2e99b49
Author: car <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 a07c853a550b3f5f0c16c965b749fe956444ad77
Author: car <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 3dbbacf2b3469a3af4c83a12837a00f3f4fa3adf
Author: marc <marc>
Date:   Fri Jun 2 22:58:53 2000 +0000

    extern c chuck you moron

Src/C_BaseLib/ParallelDescriptor.cpp

commit 74f77cf3177e042b851323800882206b7268b234
Author: lijewski <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 7d91c82c62913cd4a8d4863a4b7309bce47dc75b
Author: almgren <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 a7dec4a8b5ab2a2f2118dd0b655a3106bb1fae84
Author: lijewski <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 20ec429a523487e42e602a968f0a569b3ea2d248
Author: car <car>
Date:   Fri Jun 2 01:04:12 2000 +0000

    Bad BL_PD_ABORT defn

Src/C_BaseLib/ParallelDescriptor.cpp

commit 1cb8722dbb90f3d20629386caf82300e6fa1af3c
Author: car <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 f77e6c9871ec9ac4afdc8644707a865d4a5af587
Author: car <car>
Date:   Thu Jun 1 23:09:28 2000 +0000

    use ksh in Make

Tools/C_mk/Make.OSF1

commit b26efc2f2c26507d4ebfa610d59b250ba9a439fa
Author: car <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 9f5057babfbfa106058b6b6e46fdcaa0eac0bd64
Author: car <car>
Date:   Thu Jun 1 21:39:54 2000 +0000

    using ParallelDescriptor::Communicator()

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit e8d07b45053e7c02eefcd98244ab3fcba947f75d
Author: lijewski <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 308defdbb9389e44df2aaa3ab513202b40072530
Author: car <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 a8cce260432ec0be7f7010bd381a447da481657a
Author: car <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 1a575fb977ad1a16c7278d8d0273246fa438a4b7
Author: car <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 1c3924a702b48b8b0f28328c42334f2aadc29e13
Author: sstanley <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 b4e8061a3aadbdbcc43706537463e8a966e420a2
Author: car <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 f34d641c4ca95250da82927596f67a8b9f283bd3
Author: car <car>
Date:   Wed May 31 20:35:25 2000 +0000

    const-ness issue

Src/C_BaseLib/Geometry.H

commit f5fd13c1a4b0d7154045083dc30f4f8d1eaec8cd
Author: car <car>
Date:   Wed May 31 20:33:40 2000 +0000

    Silence a warning

Tools/C_util/WritePlotFile.cpp

commit f4573b187ad5a7ec137453bec3c16cbebb6fba98
Author: car <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 8a04fd129a260aeebe380628a6624c5e9cc4148a
Author: lijewski <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 239bd369f22b4b1a9bd595ef767a14c1cbfeda93
Author: almgren <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 dc30bac210f78b61d6f82a74847796000bb8e3a1
Author: almgren <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 c39122c9947fd2e4095f05a82bab3ca61c0877ec
Author: car <car>
Date:   Thu May 25 15:49:25 2000 +0000

    .cvsignore

Src/LinearSolvers/C_CellMG/Test/.cvsignore
Tests/LinearSolvers/C_CellMG/.cvsignore

commit dd54a85ea8bbefa3d1e18dc400cc26fbdb365b9f
Author: car <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 2589500e6dc0e913bb4c6a5fa2cfaf148e1e24df
Author: car <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 9955fb74936e909a025eeb35ed00514a0feea195
Author: lijewski <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 1fd6366c53c02eb4d7b8e82b4599c956b895814c
Author: car <car>
Date:   Mon May 22 23:19:24 2000 +0000

    support for hypre

Tools/C_util/Make.package
Tools/C_util/WritePlotFile.cpp

commit 56142a525c921619049c0f11a898ea7cc8adf6fa
Author: car <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 56d8e763bda334f5181b2c59f3b9740132611e8c
Author: lijewski <lijewski>
Date:   Mon May 22 20:14:25 2000 +0000

    Added gt.sas.

Src/LinearSolvers/C_NodalMG/files.3d

commit b04f4e490151fc6bf22e8dd778698d323dbe6561
Author: lijewski <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 031bd92f81e1cac71df7c3d3570d71ec7946c952
Author: sstanley <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 d3fd564b846e3a11c8f86fea178eb00641388e62
Author: lijewski <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 b6624f5e5aaec8fbd6d7aebed5122e9cc42e6f04
Author: lijewski <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 b6d074d4446223f7e778195973e06f0674ce386e
Author: lijewski <lijewski>
Date:   Thu May 18 19:55:44 2000 +0000

    Made the stencil default to cross.

Src/LinearSolvers/C_NodalMG/inputs

commit fd687731b2e948f56705cf0794a5f6a6a2f15db6
Author: car <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 9ba7a19ce4d3566ea1139fe5f8098c00e3289deb
Author: lijewski <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 457c685cd36b01b726a2841adfed80999eb4b579
Author: lijewski <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 007a205985d4d7e961441b2228808621ae7f9d20
Author: lijewski <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 ef101924e7879d6432b27d28ae3b03d5533b9151
Author: car <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 314b33ed6678801845126d201f96b73fc2a95c14
Author: sstanley <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 7b3f7e7e8d82519ed8b2dbae21642614f4bf7638
Author: propp <propp>
Date:   Thu May 4 23:43:49 2000 +0000

    reordered build_sigma a little bit

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit dd52c5409c8b8383edde055979be067fc7975d9b
Author: car <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 8d0eb7d44d6e6bf6fc1bd0a06eebf4ba840f14be
Author: sstanley <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 6cdc270f3504b3e6e24a3cc42fd604284ac71ef3
Author: almgren <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 5fb5b29f48fb77a50909a653072799e70654ce04
Author: almgren <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 968da1585946d2b95d8148cf6198eae649aecf36
Author: propp <propp>
Date:   Wed May 3 17:12:11 2000 +0000

    changed default for NAMESPACE to be FALSE

Src/C_BaseLib/GNUmakefile

commit b05468c094c5dacb42a2955a2967f0103d078b2c
Author: propp <propp>
Date:   Wed May 3 03:36:40 2000 +0000

    fixed bug so libraries would be built correctly

Src/C_AMRLib/Make.package

commit ddcbd3c91bd0ab652c25d895426c665e913c0be5
Author: sstanley <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 0216b6bc6ccd510a84edc9a7b9d77dfac3904c3a
Author: car <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 e8162fe988f77c114335859ea22c9fc75bb89111
Author: car <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 8d9b198173a3b3f9a60c7c8acba9d54dbcb5a6dd
Author: sstanley <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 bea13d73c116399cefb5f8499b65836094a9b8bc
Author: car <car>
Date:   Mon May 1 17:53:24 2000 +0000

    Remove Assert.H from Make.package

Src/C_BaseLib/Make.package

commit 83c8e3fb087c841c6db169d349646d0e4668f8e8
Author: car <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 2abcda3808813c389afd8ebf4a82698381845db8
Author: car <car>
Date:   Tue Apr 25 16:29:56 2000 +0000

    more namespace fluff

Src/C_BaseLib/FabArray.H

commit 9984efe981b0b4f9746734f4134e8cb84dc94c24
Author: car <car>
Date:   Mon Apr 24 18:00:52 2000 +0000

    missed one

Src/C_BaseLib/SPACE.H

commit a4f8a4dc4072af4e35e388fc08f6b2645a805559
Author: car <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 bf1b07db7b269afee8014cea11d86ecbb29ea04a
Author: sstanley <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 5096152affdbb76912a4b38d46f6848fddb13342
Author: sstanley <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 31d67be32f3e1a796c0177691faf2b9d41cfb3dd
Author: sstanley <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 56c07943d98d47e81f1bcc1471cdfd6ce9c2d7dd
Author: sstanley <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 fa8772fac5754a89926dcea4ac48f933c38f6a6b
Author: sstanley <sstanley>
Date:   Fri Apr 21 22:28:16 2000 +0000

    Elaborated on the documentation for SlabStatRec.

Src/C_AMRLib/SlabStat.H

commit 15415b1ff581896da082f581c78f0a82791da9cb
Author: car <car>
Date:   Fri Apr 21 18:46:06 2000 +0000

    fix for g++

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 8ae5f622ae837d66bf67e4a7aeb7b598837839a7
Author: sstanley <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 fbcdca2331ab99004058a52ba730ec54ac698116
Author: sstanley <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 45e21172c6f8bbe1012bef85eea51e4d7777f8f7
Author: car <car>
Date:   Fri Apr 21 16:23:32 2000 +0000

    *** empty log message ***

Src/C_BaseLib/CoordSys.H

commit 3e927f22569018c2067cc93d2dfe998c650c398e
Author: sstanley <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 f1891ab2813d2f172d53506c152d1b76726c541d
Author: car <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 78d0c11815866e83ac6f224672787eea8b1bd3a7
Author: car <car>
Date:   Thu Apr 20 17:46:47 2000 +0000

    noquotes in fortran

Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F

commit 48343ad8bb3dd3a5c0cc8165b057a2b8bd864cba
Author: car <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 a69bffa413ed30002881489a30911b184a6417d0
Author: car <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 7c707ab930ac1bb7cc2ffa8077342797d9e14f35
Author: car <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 6e388474f9521a84ff4d0c134c0041049d5fbe4e
Author: propp <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 4ccdb9f8d7620c118d509cec3cec22cd78c884c2
Author: lijewski <lijewski>
Date:   Fri Apr 14 20:45:48 2000 +0000

    Fixed some bugs.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit e5e3970b4ff125735ca2240bf3e997de973fd071
Author: sstanley <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 1fbd50443b55845db851d345f4e27528f5a3bf29
Author: sstanley <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 075e18f56eb448f0de23d82d8a09398324a12bb4
Author: sstanley <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 f282bc9a96fc5580d9b04f79c856732fe5c9f1e1
Author: sstanley <sstanley>
Date:   Tue Apr 4 18:28:59 2000 +0000

    Changed the box definitions.

Tools/C_util/ViewMF/viewMFdiffHardWire.cpp

commit ef3b5b43de8f27727cacb4201103fd0ebad46fb5
Author: vince <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 185a90916847c0bf1622ab06b51e0b1b8ad54b9b
Author: marc <marc>
Date:   Mon Apr 3 23:13:03 2000 +0000

    ifdef out os stuff...see Utility.[H,cpp]

Src/C_AMRLib/Amr.cpp

commit 3bc827d18ad13b949228c68ca3dfd7cc190b118a
Author: marc <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 ab992492c3e1503dd893f52eda2da9e275b5a904
Author: sstanley <sstanley>
Date:   Wed Mar 29 23:05:54 2000 +0000

    Added the ability to build in place.

Tools/C_util/ViewMF/GNUmakefile

commit a645a0a896396b6ea3a2f838d91926e63201018a
Author: sstanley <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 66df9cb337752c31731df6e8b8a4bae76684a13e
Author: lijewski <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 9f6e93867d34059e5a59c9b89266b35a85a09e6d
Author: marc <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 efec130eeb990fa72f6dbbf603fbb46b6868de0c
Author: car <car>
Date:   Mon Mar 27 20:06:07 2000 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit fff5422e32ad009632a0f22b8137f0d65c970274
Author: lijewski <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 0ca56248cc2e76335d40be7ec8fe06fbf95e7388
Author: lijewski <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 cfc544e0ab50402d21189081cbb20391d8407b53
Author: car <car>
Date:   Fri Mar 24 18:13:19 2000 +0000

    Removed path dependence of tarch, tdevice.

Tools/C_mk/Make.mpi

commit 7de49d10798f92125ff3c9e554be2ff522d5f97f
Author: car <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 033380adeff01261e4877efb777ead80b4d5d3f5
Author: sstanley <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 8a7acfa63bc5ff9421d0a958ae92a1499e094f9e
Author: lijewski <lijewski>
Date:   Thu Mar 23 21:39:06 2000 +0000

    Turned off a couple things.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit ed4f5b615e985364d7ca0ccef78b26b17d955672
Author: lijewski <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 ef83e4f5fb2f6a9550c893c0e3d7033a58071ba4
Author: car <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 5c950afd4f8d5ca1d8d4fa19f35b94bfccbca7d2
Author: car <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 74d1d8cdced2e6e778d74084a41f3feb5554736b
Author: lijewski <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 db900b3622a1cfe3818fdb4246e9f45a009d8150
Author: lijewski <lijewski>
Date:   Tue Mar 21 19:24:04 2000 +0000

    Added INCLUDE_LOCATIONS stuff for OSF1

Tools/C_mk/Make.mpi

commit adb0b333bc782cb6e64f12806b593737511f5b6a
Author: marc <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 6d0a0b88b2c90b1e43584bddbd84650e384a3b82
Author: car <car>
Date:   Fri Mar 17 21:58:59 2000 +0000

    k

Src/LinearSolvers/C_NodalMG/hgdebug.F

commit c105d321e7a567f455b8e27d7ccddc92952fbbe0
Author: car <car>
Date:   Thu Mar 16 23:15:07 2000 +0000

    Added BL_NAMESPACE support

Tools/C_mk/Make.defs

commit e9064ad02a1bcb7c99f22c4cc885520670db46c2
Author: car <car>
Date:   Thu Mar 16 23:13:40 2000 +0000

    clean is now a double colon rule

Tools/C_mk/Make.rules

commit 1fafc6bdfa2c066cfc4ab1a55b6567082f9d90a7
Author: car <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 e8767a39975a7bd70f6973b731a843b620b98406
Author: car <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 e060b093117da08f4561969e2c79a44cbe0ee34a
Author: lijewski <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 acb484add24c484b42cd61a414a248fa0650aebc
Author: sstanley <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 64561173425db574007378992aefa6b9dd3aefa6
Author: car <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 bdc4cbc132e6aad7456cc52f82a918ee93c688c8
Author: car <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 b6b724239029cc2c7aa51377c56373a5582d8f31
Author: lijewski <lijewski>
Date:   Wed Mar 1 21:58:51 2000 +0000

    Upped the precision in checkPoint().

Src/C_AMRLib/SlabStat.cpp

commit 342fcf82cf3d27395f32718cff6d8def2661f091
Author: lijewski <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 09f3631fc25c4e75e4b93de62fcc3ba9cd43f703
Author: lijewski <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 05e9477560a1ae935431c6d689acd477dc2a944d
Author: lijewski <lijewski>
Date:   Wed Mar 1 15:43:03 2000 +0000

    Defaulted another argument.

Src/C_BaseLib/VisMF.H

commit ed54762ea1f5d1c0e2c233a91b486707798831c3
Author: lijewski <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 82cd39b725038910aa2053c79ccfb71b13b6634a
Author: lijewski <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 db90940911dd2d04793b114578e03a37af333675
Author: sstanley <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 99c69312d60706098610b4abceb7dc6a5d708695
Author: vince <vince>
Date:   Mon Jan 10 23:55:15 2000 +0000

    Added support for yukon (ARSC).

Tools/C_mk/Make.defs

commit c5d2fa7261f922124c2264b1bc280467d15bc6c1
Author: lijewski <lijewski>
Date:   Thu Jan 6 19:03:27 2000 +0000

    Fixed docxx comments to compile with latex.

Src/C_AMRLib/AmrLevel.H

commit fe54f1a5f3fcf4ee36cf32a2c0e03651742e5f8e
Author: lijewski <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 8bc824dd2efc137310bbbfd2d7d2c4b698f9a3e4
Author: lijewski <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 a226071ef8a678d2b3682d5a85d51f3d5785800e
Author: dailey <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 ec89f325a030741328fddce8287479cdf6f90892
Author: lijewski <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 0049ce11806014c804da388d1d51dd4ea6e629e9
Author: sstanley <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 c388fc314dc1d5f8fa09cb9df04764ccb7419f94
Author: lijewski <lijewski>
Date:   Wed Dec 1 16:37:24 1999 +0000

    Shut up a warning on SGI ...

Src/C_BoundaryLib/BoundCond.H

commit 8e31696d339ce3c929576ad0ca3a57a03aa29829
Author: lijewski <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 079dbca7c1182cf7b0805d0d0fc2609009bacc8a
Author: lijewski <lijewski>
Date:   Wed Dec 1 16:16:45 1999 +0000

    Shut up warnings ...

Src/C_BaseLib/BoxList.H
Src/C_BaseLib/MultiFab.cpp

commit 1b4ffb7fcec75008698513831d70378eb932c061
Author: lijewski <lijewski>
Date:   Sun Nov 28 19:48:51 1999 +0000

    Don't try to read .profile

Tools/C_scripts/compressor

commit 896cd1e1f83cfcbd6afb028d7eaccd94e74fd047
Author: lijewski <lijewski>
Date:   Sun Nov 28 19:48:22 1999 +0000

    Mod to fix bug on T3E

Tools/C_scripts/compressor

commit b9442eceb14157c1746e91d016b7d9fe25e1d843
Author: lijewski <lijewski>
Date:   Fri Nov 26 20:02:41 1999 +0000

    Strip out any possible tar files.

Tools/C_scripts/compressor

commit bb4bfa388a42c423f3e00ff8951b5f3f663a3763
Author: lijewski <lijewski>
Date:   Sat Nov 20 19:41:38 1999 +0000

    Direct error output of `ls' commands to /dev/null.

Tools/C_scripts/compressor

commit bd12e5e077580de9a2bf4e6d9882547830a64741
Author: lijewski <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 802aadaa4eec261a2989edafa482647d83ca86ad
Author: car <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 b8a7f653625276809d59433c77e51156bd53912d
Author: sstanley <sstanley>
Date:   Thu Nov 18 21:29:57 1999 +0000

    Minor change to fix a documentation problem.

Src/C_BoundaryLib/FabSet.H

commit 8ad0e941bfeaf14750d77a3b02ff8f42206891f5
Author: car <car>
Date:   Thu Nov 18 00:27:51 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit aa804eb4c739d97239bb6cb237d7fb46954a52c3
Author: car <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 5abd2e6612fedd66d8535ca5bd04aff13c16dcc2
Author: lijewski <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 8152fb10af5b5fe642c2b1cf98c7f612c35630fb
Author: lijewski <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 2187698c5953534ab99adcac5c4d0c94b31922d5
Author: propp <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 2dde6cf4d4a2fa4e1155c84e715992732522a6c4
Author: propp <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 5fee1f8bbca752c4022f0f1f12ad898ac179181c
Author: sstanley <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 3339ee0e4fca84dfb439a6a620a66ff878fc1e02
Author: sstanley <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 d0782c216b9ed3ef52f2b239e881940bbdb5813a
Author: lijewski <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 35a430931fb16e61d00ccaa9526e6372a3d6744d
Author: vince <vince>
Date:   Wed Oct 27 21:24:40 1999 +0000

    Moved a flag.

Tools/C_mk/Make.T3E

commit f8175b0a85867e5c14cba1b5053e8ccab5e77b5e
Author: marc <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 63d43bd126d580dea29e56c0689d66c0f6a2892d
Author: marc <marc>
Date:   Mon Oct 25 18:29:54 1999 +0000

    Add optimization to FFlags for opt.

Tools/C_mk/Make.Linux

commit 0b72b27aeb2e526cc9c422dcd7112ddaff95c2a5
Author: lijewski <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 ab213bd7f47d5cc1df10fc8fdf3105ffd3bd17e0
Author: sstanley <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 fcae20e9d22d631e3df933b6acd07340ccfeb5a3
Author: sstanley <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 79af38554c4547d98a2ce51b7f2805a8d6bc0543
Author: lijewski <lijewski>
Date:   Wed Oct 20 18:25:13 1999 +0000

    Added Execute().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit af39a4c0f6c37917ff821655acfa97c68b470910
Author: lijewski <lijewski>
Date:   Wed Oct 20 18:24:58 1999 +0000

    Added amr.tar_and_rm_files ability.

Src/C_AMRLib/Amr.cpp

commit c61ae6e861c5152c96b46054b68ffecb04408031
Author: vince <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 5db41fa860ddc95aa66479d2d6efaf91242e098a
Author: propp <propp>
Date:   Fri Oct 8 20:54:50 1999 +0000

    added plotfile_on_restart option

Src/C_AMRLib/Amr.cpp

commit 0c1118de8b708494220111d1fd7442d946cc94d8
Author: sstanley <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 9d6dc43ca6d80bf07d960543d1988244fbf3c0b6
Author: lijewski <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 b02bf9e5c3c335c53a8112f7c00cc7647c5ce4b9
Author: lijewski <lijewski>
Date:   Thu Sep 30 14:55:53 1999 +0000

    Removed cached MultiFabCopyDescriptor junk from MultiFab.

Src/C_BaseLib/Geometry.cpp

commit 67cfd59cc12cfa08432d4b50dba5c481518c5cf6
Author: sstanley <sstanley>
Date:   Wed Sep 29 21:46:08 1999 +0000

    Modification to fix compiling on the T3E

Tools/C_util/ViewMF/GNUmakefile

commit 6cdf505ec848bea39196f0bcc0d3ea8b9b2fa8d2
Author: sstanley <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 f578cf4d2545f874ed5e7ddac8c955a5faa4cf38
Author: marc <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 b9d28d071226b283dfa27ad809fe1bfd5c51a62a
Author: vince <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 7b64d830b9b0f47c670c0753dc8eea5d225f0b23
Author: lijewski <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 605eda1dee02f0a18c549eee0b5ca6c5593d45c6
Author: lijewski <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 018100fdb505b1405457d1123949ed3e29ece39e
Author: car <car>
Date:   Fri Sep 17 17:22:47 1999 +0000

    tweak

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 2ef76af06a6eda4ef7c2f64227b2ec7c422ac852
Author: lijewski <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 4fe867dd39d882dc1d0202d56b0448f3a8bef39a
Author: car <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 1b6529088ee98e29dec423a935befc7ebbae9aa2
Author: car <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 352c1dc7e986a3c1ee627c6206e3fdd3747bf395
Author: lijewski <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 a58c280f46a173ea246dd5ee5874517f8fcf9fa2
Author: lijewski <lijewski>
Date:   Fri Sep 10 20:53:01 1999 +0000

    Added -fpconstant to FOPTF and FDEBF

Tools/C_mk/Make.OSF1

commit 764f7988442df9d2a997ff5c2ef8217624b54db8
Author: almgren <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 e4c434d00c78e3acbe417bd1c178b61a500c8125
Author: sstanley <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 5acf14a77f8295927dc0350151294d11faa40a15
Author: sstanley <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 9d839819e4a92939ae74ff6120424df796101a1c
Author: sstanley <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 73ce415273ea2a38880e2b19a39934a78cad9cb9
Author: lijewski <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 9de3368c7c73af210bdc2fca8c9a1f7ccfa37bf8
Author: lijewski <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 ebdd64399ebaa8a858163c1c5719075dc7ba2d0c
Author: propp <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 a9d73ea4f42726e5bfce737be2db333a2505d5bc
Author: lijewski <lijewski>
Date:   Wed Aug 25 17:52:33 1999 +0000

    Fixed bug regarding usage of ConstFabSetIterator.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit 412b91112760ed7757ca971d49b3fd1cb6db2202
Author: lijewski <lijewski>
Date:   Tue Aug 24 21:02:22 1999 +0000

    Use new hfiles with KCC ...

Tools/C_mk/Make.AIX

commit 8d94aa25cc0a76a5be4e77a1c97e79c16bae61a1
Author: lijewski <lijewski>
Date:   Tue Aug 24 20:08:46 1999 +0000

    Simplified some settings.

Tools/C_mk/Make.AIX

commit 6572319b9288c8489773948dad885b68cbd7d7ad
Author: lijewski <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 c7bf6a9576a62e5bb2b9719a0326f7a49d71d4a8
Author: lijewski <lijewski>
Date:   Mon Aug 23 21:19:58 1999 +0000

    Added tokenize() ...

Src/C_BaseLib/aString.H
Src/C_BaseLib/aString.cpp

commit 62c128ae9ad423fdc0355bba4fcc0118b1e7f74f
Author: car <car>
Date:   Mon Aug 23 21:16:49 1999 +0000

    support for Geometry

Src/LinearSolvers/C_NodalMG/inputs

commit ae6c9ca046532e51eee3966977b0697af4ea3d97
Author: lijewski <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 90f6047d28de926b311f0980d31ac12255c082c8
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:52:55 1999 +0000

    Removed --no_restrict; Crays header files use it :-(

Tools/C_mk/Make.T3E

commit 7268f829d58f541f4818e89dbf6c107566d8805f
Author: lijewski <lijewski>
Date:   Fri Aug 20 17:38:02 1999 +0000

    Added --no_restrict

Tools/C_mk/Make.T3E

commit 05ae30bc0ac3d53c6486da44650ed977af1d314d
Author: lijewski <lijewski>
Date:   Thu Aug 19 20:16:32 1999 +0000

    Fixed yet more memory leaks ...

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d63773a55902366331fc4ff5db69ad6ddd988379
Author: lijewski <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 07d6920c843ac7bc8280c1a7b18e7bdb9f30e510
Author: propp <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 ca572fe43cb09368231fcc1c62b22a96df02a26f
Author: propp <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 3ea90c461a96f9b17fce3a66000500c9850a097c
Author: lijewski <lijewski>
Date:   Wed Aug 11 19:52:05 1999 +0000

    Added FOPTF+=-O for default case

Tools/C_mk/Make.Linux

commit 287493048f303bef45dc3b2cd800d47f89e07bc0
Author: marc <marc>
Date:   Tue Aug 10 00:12:42 1999 +0000

    Generalize for prversion/parallel junk

Tools/C_scripts/dsp.mak

commit af60930bbbca3c51d36e5224b0030134fdca8cb0
Author: car <car>
Date:   Mon Aug 9 16:44:41 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 17a6b3dede33c235b64f9e31dddc76075af403ff
Author: car <car>
Date:   Fri Aug 6 23:10:05 1999 +0000

    bndrylib is now needed

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit dd8c4d29a6897f79e44a32e744fba45b53567438
Author: sstanley <sstanley>
Date:   Fri Aug 6 22:45:28 1999 +0000

    Fix to BoxArray::contains(BoxArray ).

Src/C_BaseLib/BoxArray.cpp

commit 7379d6123cead861f671e0e1de6c42d1fdda149c
Author: propp <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 84dbffaae444602f2fc81f30a6b581c11d81c6c2
Author: propp <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 0e22c47508422d5adaf8116806e92a6c68f9bbbd
Author: almgren <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 c25c2949730b5fd4b6b51929488923958961ff62
Author: almgren <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 39345ec178dc8788a03886f9049aed3005ec9c33
Author: propp <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 c4f9a9b48ecdadf0ae17fa8b47f7b1c11f6f2c21
Author: almgren <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 1b73999462c5aeddcdea538abd3d2ebb4f9c9923
Author: sstanley <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 8d7c1542cfbe87f1004e97971c80773f5a0080a6
Author: almgren <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 085c7d251738bf147db320858a911009a0abc4d8
Author: almgren <almgren>
Date:   Fri Jul 30 23:46:06 1999 +0000

    Warning message in hgfres.

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 0ffdc455e93303d62bf7bdd78e68926a06587792
Author: marc <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 ec51026699faddbd4e59224ed6a98d49b87a5701
Author: almgren <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 4973823218d00669f2407bb9d2817696841fc867
Author: marc <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 aaa4b1ad95c6690304f635dff6d58e150f47a4c2
Author: marc <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 76102e4dedb62c3b69e33f9317405fb983c539c4
Author: marc <marc>
Date:   Tue Jul 27 17:34:06 1999 +0000

    Make physicalBndryTrpes available to Fortran

Src/C_AMRLib/BC_TYPES.H

commit 0385bbc21d4edf51415323a01ffaa76d1fca1e07
Author: lijewski <lijewski>
Date:   Mon Jul 26 16:59:42 1999 +0000

    Updated a comment :-(

Src/C_BaseLib/ParallelDescriptor.H

commit d7ced55b981c9875bfab74adfa80b04e1d88eb78
Author: almgren <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 99a523be56448807a55a62f76744350225832fc1
Author: car <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 37ab5cd15d9b977fd70b868c53191a3ce6fb1a10
Author: car <car>
Date:   Fri Jul 23 21:28:31 1999 +0000

    saves work in serial

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 4c67f250cecd826ecea7465c307aa8a11a72e4da
Author: car <car>
Date:   Fri Jul 23 21:28:00 1999 +0000

    fix for array bounds bust

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 1175c5dde1bd9a208a328e6c2d3a78b3a8620dff
Author: car <car>
Date:   Fri Jul 23 17:56:40 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit b9d5aa0f3178c105f8b751e272d09472f29848c9
Author: sstanley <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 940436807b005c4a6b62f40dc0d0029ef2712ccf
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:07:38 1999 +0000

    Output CArena stats ...

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 7b7995f45f15e1a2a26ab5bb2c3d5de363935899
Author: lijewski <lijewski>
Date:   Wed Jul 21 21:06:08 1999 +0000

    Oops -- forgot to remove a commented out #if

Src/C_BaseLib/CArena.cpp

commit 427dd1774924ee043a5a258b1d0621465d59c6ce
Author: lijewski <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 a123cce9e549467fb7003813e0b3e8eb225e3873
Author: lijewski <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 cbdb16f824aa372a663cb64b90b9d7000642da32
Author: lijewski <lijewski>
Date:   Wed Jul 21 17:26:08 1999 +0000

    Removed commented out line ...

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 6175dd27fa7f655896b3232e64de1a6a7c193c18
Author: lijewski <lijewski>
Date:   Wed Jul 21 17:20:34 1999 +0000

    Got memory mods working with periodic.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 6624dfe32d317b0348e25317813c058b28615777
Author: lijewski <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 e8573b9fb11b5dbea4adea3edd09f808c50165c8
Author: lijewski <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 8bb5238628b51e60b4cc30fa9016603a30e0566c
Author: almgren <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 7a3313c6a3b74b66f1eb79e056474797bfc5cd7f
Author: lijewski <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 5f9df0de7d34a4a9fb1ce96dce917585ed898ca7
Author: lijewski <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 5a71b010bf48cccadb84971acc30d3183d63f88d
Author: lijewski <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 58dc566e89193d5b3099c8577224ae481e23a06a
Author: almgren <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 e6e4cd1fe4e58d569a6285b92f5f87e7602357c2
Author: propp <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 67482dd53b9f8b3847f28d6ccca6d73d15bcfe92
Author: sstanley <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 cbad680fb7b5a8fe0aa422bb55a9837bc0cb4591
Author: almgren <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 1aeb22504c752b1ff8a9718f1a0c549d1bffaab2
Author: lijewski <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 b0f2dab58130a1e27467df446432fa1034740b4b
Author: sstanley <sstanley>
Date:   Thu Jul 15 01:37:02 1999 +0000

    Corrected a couple of the Docs.

Src/C_AMRLib/StateData.H

commit 27d4faa419bceed56e8ab331901d89343eb87579
Author: lijewski <lijewski>
Date:   Wed Jul 14 23:06:15 1999 +0000

    Did copy constructor correctly.

Src/C_BaseLib/Geometry.cpp

commit 2848911cdfca739d7e9d7db5552f44309a364c41
Author: lijewski <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 5715ddd56a2cb141c28ad272aa3a7cedff4c6cbb
Author: marc <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 00a77cd7c3a034d068c1e50212d4438f4d9ce258
Author: lijewski <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 1d714d8fde0e59f91917197daa138750fa306fdd
Author: car <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 4af45f42abd2696dc704c0a336df3ef6d78c92ce
Author: almgren <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 f42d05541b369b027e5faeaf80d784a516527de7
Author: almgren <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 e6583456a216291beb56d44444565fbfc481298a
Author: almgren <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 0b5afd0c298ea89568e7661252fdcb0de39f1f60
Author: lijewski <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 af7a48d174f6b9a2b0702debcec1adfe9e5d2b88
Author: lijewski <lijewski>
Date:   Thu Jul 1 19:44:49 1999 +0000

    Added ReduceIt() to fix bug with how the List<RunStatsData> is reduce()d.

Src/C_BaseLib/RunStats.H
Src/C_BaseLib/RunStats.cpp

commit d244437c2521900c7ee2849375fd3b0fa16716f4
Author: lijewski <lijewski>
Date:   Thu Jul 1 19:44:04 1999 +0000

    Got rid of old-style cast.

Src/C_BaseLib/VisMF.cpp

commit 318c72fea2829937893b62e3b099faa7b8e46749
Author: lijewski <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 abd551b8b1b26cba71ef4d411ce18e0fe356a93a
Author: marc <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 13c93d37c26c1dffa76d6b4594757b16b7fc9788
Author: almgren <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 dc3ba8aae6dd9504bd41dedb0adfc8679ceff080
Author: almgren <almgren>
Date:   Wed Jun 30 21:43:29 1999 +0000

    Removed already-commented-out code.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 576a1482e0342df5f5b700ad81c33e8b72056fc2
Author: marc <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 349bf5432dce1e3f54bdb1f19400bf1a21e6273f
Author: car <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 965a59eaec01154f96acabb48828390c05d9dc43
Author: car <car>
Date:   Thu Jun 24 22:09:47 1999 +0000

    Bone headed IntVect usage

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 2b4aa326408155a0800ece339b36090cdc1db99d
Author: marc <marc>
Date:   Thu Jun 24 21:21:55 1999 +0000

    Oops!  src was written as rc...

Src/LinearSolvers/C_NodalMG/hg_avg2d.F

commit 1e81f608e8fed61141354b1d902604cca7c73dfc
Author: car <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 94aa9fea94d25fa296153b4a74335c894a966502
Author: lijewski <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 9bf486f75d3af50efe414648b8805a7ae2bf08f0
Author: car <car>
Date:   Sat Jun 19 03:57:55 1999 +0000

    added hg_{irecv,isend,test} to runstats

Src/LinearSolvers/C_NodalMG/inputs

commit 5b8c12083923d849da94702efe0d13c145dd5abe
Author: lijewski <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 991554fe9e910de0287b37b01baf19cdf16a7cff
Author: lijewski <lijewski>
Date:   Fri Jun 18 16:01:57 1999 +0000

    Some cleanup.

Src/C_BaseLib/Geometry.cpp

commit 6d3d2bc4664ae760862f74de138de73cbdbb4e84
Author: almgren <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 f6153de4923242cc3a4aae4458315ba549b75b9d
Author: lijewski <lijewski>
Date:   Wed Jun 16 22:13:03 1999 +0000

    Removed some dead code.

Src/C_BaseLib/RunStats.cpp

commit ddcd7450218dd7021bc8ba09a4e0e98b8f528a72
Author: car <car>
Date:   Mon Jun 14 17:07:26 1999 +0000

    defused loop

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 4fb6699fa567c11d96812c69a107a15b4e117555
Author: marc <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 54b1a15785f6a07bdd0deb40ce8c0ef790690424
Author: almgren <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 749ace3c9a45f23f6d16c382b45f1ee9f0b12159
Author: car <car>
Date:   Tue Jun 8 14:39:54 1999 +0000

    *** empty log message ***

Tools/C_mk/Make.mpi

commit 190c9d8a05d5eea029a6bf606f0d69b20c4f7c17
Author: marc <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 87b2282ad53ac294d6011e4184a9b34a17a6fb3a
Author: marc <marc>
Date:   Mon Jun 7 20:57:38 1999 +0000

    Remove rz assertion

Src/LinearSolvers/C_NodalMG/amr_multi.H

commit 4b520cb87e7e7a9886fde687c2314538d99ec126
Author: car <car>
Date:   Sun Jun 6 19:07:42 1999 +0000

    *** empty log message ***

Tools/C_mk/Make.Linux

commit ac3f683be06453a96cd6a7386fc71f595fbed368
Author: sstanley <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 1e70bc2ecad3499bd5551aca7b4272d6f6410df8
Author: sstanley <sstanley>
Date:   Fri Jun 4 01:03:25 1999 +0000

    Modification to make it work on the T3E.

Tools/C_util/Convergence/GNUmakefile

commit bbaa614cf87692046362f8d898f8c34eb9a78d5b
Author: sstanley <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 ca85091137aeadd821e1029db7537c91c02fece1
Author: lijewski <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 c91bd3dc783b4dc62d4439e4fa7bb2fcd3e5c486
Author: lijewski <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 b549c7163e84148f33e622429e9ae6f1fa406736
Author: lijewski <lijewski>
Date:   Wed Jun 2 19:20:53 1999 +0000

    Tightened up some assert()s

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit c7b4e787241fb86354a5f83c0e08d9f46147eb03
Author: sstanley <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 be9b03fb026eecdc7e66faaa9c3ed54630a9ad94
Author: sstanley <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 6c1b5e28509c5a5952ee21276775524cc1b21928
Author: marc <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 92ff35add275d12b0c8efb108e9b3a525e58f980
Author: marc <marc>
Date:   Tue May 25 23:09:02 1999 +0000

    Fix include for WIN32

Src/C_BaseLib/CoordSys.cpp

commit d02b9a2f5793573a88c05460ce520d34b4688dc3
Author: lijewski <lijewski>
Date:   Tue May 25 22:02:20 1999 +0000

    small bug fix ...

Src/C_BaseLib/FArrayBox.cpp

commit 93f07f042b4a599cae4c370a660f423a04b63a80
Author: car <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 680293170af6837d9f6c60290771642101577544
Author: car <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 ec6c3a95d7f3489c56c314b718756e7130510e1a
Author: lijewski <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 865cc988f6b6695b92f4dd437e07d0dbc41a0dc2
Author: car <car>
Date:   Mon May 10 21:32:52 1999 +0000

    tune for absoft, g77

Tools/C_mk/Make.Linux

commit 3e81b537891d329618bd0b2787b3c163aba8c6b3
Author: car <car>
Date:   Mon May 10 21:26:31 1999 +0000

    tune for absoft, g77

Tools/C_mk/Make.Linux

commit 48267356f3e0676ee1a0c4c622e5d3d8dd254c79
Author: car <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 375320a8cca7c1c271a415afc5213f8b21097323
Author: lijewski <lijewski>
Date:   Mon May 10 20:44:50 1999 +0000

    DBL_MIN -> -DBL_MAX and likewise for FLT_???

Src/C_BaseLib/MultiFab.cpp

commit cecf9555c742079a438dbc347512f5a45e6ecb68
Author: marc <marc>
Date:   Mon May 10 20:31:14 1999 +0000

    Move logical reset inside loop to behave correctly.

Src/C_AMRLib/Amr.cpp

commit 183cca625a6e1c59eb0575c33e1a82055b6bcb4a
Author: car <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 91d741305621d8aa66980578b66b326c18f0d8b3
Author: car <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 d2593cabeb7e1e6aca63c8a61cc7e867d87c2d85
Author: marc <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 9332cb1d75799da5b2255c383c7aaf8c9272a4b1
Author: lijewski <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 b144514c4e4c42cc4cd6f9fc8842c8f4c1e57fb9
Author: car <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 e0bfa7e6c661509f626279637f1bffc4d33c2bb4
Author: lijewski <lijewski>
Date:   Thu May 6 16:31:41 1999 +0000

    Hack to work around array bounds error ...

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 85b36e25f94dd6db6b654b27b59d2d03089a8fde
Author: car <car>
Date:   Tue May 4 17:59:06 1999 +0000

    assertion for intersection of src,dest boxes

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit 672aa4affe33a69e8d6fae2b2dfcf84a2c5e0fc4
Author: car <car>
Date:   Tue May 4 17:58:59 1999 +0000

    ofstream truncate???

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 4918d2a0689b941ddfc63e83e4a3285f329ae28d
Author: lijewski <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 dff88d99716d60e60e5c7af4cea270c3385b6636
Author: car <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 a48ce8bab13d7269619327a42da0ce9da495a8fb
Author: lijewski <lijewski>
Date:   Thu Apr 29 20:41:45 1999 +0000

    Now properly call constructor and destructor of T.

Src/C_BaseLib/BaseFab.H

commit 7f2a6ff234b5d2447e70e97ffbaeb27d93246c11
Author: car <car>
Date:   Wed Apr 28 15:41:52 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit e35ff1504500d3811d4485feb13424bf0f6e5e63
Author: car <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 fee187bb51b0042558e6570b6a3598f65d3c5fe9
Author: lijewski <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 b95331a3184a073b2e09276851d62208f19e1474
Author: lijewski <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 f2f0e7600713fe69a614c1a0c23ea506d1f7102f
Author: lijewski <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 e76527e0fcc4ba7097a129676f639403cf3f3e5e
Author: lijewski <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 d2226550ad8e636961cad6186795c99703e8c205
Author: lijewski <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 2d1994db58454ac7eab9fc43892b1b8c56383f4c
Author: lijewski <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 956e6dc7c9f781ab7e925779aa248bd1a2751659
Author: lijewski <lijewski>
Date:   Fri Apr 23 18:06:48 1999 +0000

    Set CPP=KCC -E if have KCC

Tools/C_mk/Make.IRIX64

commit 389472e393a42f224f950b8ef9bf6c98f9329bc6
Author: sstanley <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 e6def25bc1f5131325f7f11e197a06aa2cf630c5
Author: marc <marc>
Date:   Thu Apr 22 17:13:19 1999 +0000

    YAAF: yet another access function.

Src/C_AMRLib/Amr.H

commit 008eba6bb349a379d4676c3c16a1116ffed7c0ae
Author: sstanley <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 9af4860e40088f7e8048b5d45113e122e4567207
Author: car <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 16c62036d421cd18cf32a8b8b5d64c8a4c8bb994
Author: lijewski <lijewski>
Date:   Mon Apr 19 23:17:03 1999 +0000

    Some mods to CollectData() ...

Src/C_BaseLib/FabArray.H

commit e02f36f4ee84405e825eb5f957819eeefc18b783
Author: car <car>
Date:   Mon Apr 19 00:42:12 1999 +0000

    CRAY --> BL_FORT_USE_UPPERCASE, and tweaks

Src/C_BaseLib/Make.package

commit 21379c887eaaf2999d7d365a7a467f7a9fcec737
Author: lijewski <lijewski>
Date:   Fri Apr 16 19:19:48 1999 +0000

    tune ev5 -> tune host

Tools/C_mk/Make.OSF1

commit 17d7e8093a65a4757a71e61954fc741ac5f40f18
Author: propp <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 891aa7763e0070d7627e0f75f935e06379d89c40
Author: lijewski <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 da8e89ac15866d5531b7e672210a30f345462798
Author: lijewski <lijewski>
Date:   Fri Apr 16 00:19:05 1999 +0000

    Didn't get the optimization options quite right.

Tools/C_mk/Make.T3E

commit f11d44fe599e60edbec14d663fd074ca3c6ecc07
Author: lijewski <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 3be33f442829a0928eb91a41e25b960daf9b9d97
Author: lijewski <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 0b32824a7c523abce3962d8ae529fa344957c5c9
Author: lijewski <lijewski>
Date:   Thu Apr 15 23:28:37 1999 +0000

    Added random_shuffle() stuff to knapsack.

Src/C_BaseLib/DistributionMapping.cpp

commit e5fbb05b2a460c6e00fa92be56b14267c5b62484
Author: lijewski <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 021c78705430ae0bcfb35adcca93d1dd6eb68a40
Author: sstanley <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 db17eb50b761bc1c16ca02dbbc3003529bef6fa7
Author: sstanley <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 a7ad4e0b538fcfc1a27f58b95c5f7cb1600773cb
Author: lijewski <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 7de6a9fa9237e7f986fecfb2a8b7b7f166f37b0e
Author: lijewski <lijewski>
Date:   Tue Apr 13 00:09:14 1999 +0000

    Modest simplification of FabArray -> FabArray copy().

Src/C_BaseLib/FabArray.H

commit 97d34c4f5fddc3fde698acdc3d1a96894ae2b7ea
Author: marc <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 f7b906b717b067b76404d86306294ebc153ee2a8
Author: marc <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 e40ca7b62c2adc648725205ac62f4513197525f8
Author: lijewski <lijewski>
Date:   Mon Apr 12 20:31:47 1999 +0000

    Added additional assert() in ::Copy().

Src/C_BaseLib/MultiFab.cpp

commit 3cb3de4157354bc366aea8b181236046f4776263
Author: lijewski <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 80ec22b162692f01a05c343cc8d91698dedc17ec
Author: lijewski <lijewski>
Date:   Sun Apr 11 23:30:47 1999 +0000

    Simplified FabArray -> FArrayBox copy().

Src/C_BaseLib/FabArray.H

commit a3d96dade2ede2b0aa240e0f6cf9e256c411d768
Author: lijewski <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 4d3c2612d4260d7585c2a305bcdcc6f42092e466
Author: lijewski <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 2889ea36e38fed4cd9fbfa93f2db6f384bd94ada
Author: car <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
Src/LinearSolvers/C_NodalMG/hgparallel.h

commit b36a235cce7994660b4ccd6c7f407d4b42d2d99f
Author: lijewski <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 d891e2051ec60eb1e7a96bf2c39ce7e5ea8ad5f5
Author: lijewski <lijewski>
Date:   Thu Apr 8 20:22:43 1999 +0000

    Also now cache FasSet/MultiFab BoxArray intersection junk.

Src/C_BoundaryLib/FabSet.cpp

commit 58c695d4bb3e726e4d17cc0473b355bcc51989c9
Author: marc <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 26d7d4c6a32aef5c9766e617c5f1d9da22f53f3a
Author: lijewski <lijewski>
Date:   Thu Apr 8 17:01:45 1999 +0000

    Fixed latent bug in plusFrom()

Src/C_BoundaryLib/FabSet.cpp

commit e140fe84ec172156b124f8e1bcdf95d3f15ba993
Author: lijewski <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 9cc4f5c84a0415e28bca04746bafe6a1d3e5afe2
Author: lijewski <lijewski>
Date:   Tue Apr 6 18:15:59 1999 +0000

    Some cleanup.

Src/C_BaseLib/Array.H

commit 9320d63c06e74dd08d992b2c375a2716447fcda5
Author: lijewski <lijewski>
Date:   Tue Apr 6 16:53:37 1999 +0000

    Added -M 1110 to FC

Tools/C_mk/Make.T3E

commit 669e03b1cae6a569ed4a53358dc81ea96bc696a0
Author: lijewski <lijewski>
Date:   Tue Apr 6 16:41:18 1999 +0000

    Ignore additional warning 7212

Tools/C_mk/Make.T3E

commit 67a9f87b07f096ac46ee125bbe05002b72712f72
Author: car <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 9b9a3c5bbecb23fd86e59fba2ea12602372e94ae
Author: car <car>
Date:   Mon Apr 5 16:49:25 1999 +0000

    fix non-inplace compile

Src/LinearSolvers/C_TensorMG/Make.package

commit 445852ec513aa6cb8436fdb568555b325f7878dd
Author: sstanley <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 14eea6d1d47f9ca47e9b592fa986674cb8b7bb78
Author: lijewski <lijewski>
Date:   Thu Apr 1 23:52:55 1999 +0000

    A special FORTPREP for T3E ...

Tools/C_mk/Make.T3E

commit 0104d8c5cb0499d098429666de5b1ca6baf024a9
Author: lijewski <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 e3c2cd07861c61b9ba120064d6b6fc9281629660
Author: car <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 63114453f953f3395161c6fd70336bb610cc54d7
Author: car <car>
Date:   Thu Apr 1 21:42:49 1999 +0000

    FORT_FLUX added

Src/LinearSolvers/C_CellMG/LP_F.H

commit 744636e36353492cf112e0ac17bcf514e107cc7a
Author: car <car>
Date:   Thu Apr 1 16:57:48 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 513648693bdd9e1e32afde892a2f29966a4c70d1
Author: car <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 732981adce80ec23f7154206b930b31bbdc34be2
Author: car <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 3197e5acd7a1c78758d4648992ae812d7828dd01
Author: lijewski <lijewski>
Date:   Wed Mar 31 18:19:03 1999 +0000

    Turn off message warning 1135

Tools/C_mk/Make.T3E

commit fea4352137e74279a70fd1b517eeb5fcb59662ae
Author: lijewski <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 966059b05e50352680296285480715be7185c975
Author: lijewski <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 9f410ead16efe66dd402c734a4ba8030568bbdfc
Author: lijewski <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 41ee92f803015a26b1ed2687a3e19cce133e4ea4
Author: car <car>
Date:   Tue Mar 30 00:54:06 1999 +0000

    New defines for linux

Src/C_BaseLib/FPC.cpp

commit 03396ad20ff9f08cf599c80f2375b4cfc8ce1909
Author: car <car>
Date:   Tue Mar 30 00:49:50 1999 +0000

    A first approximation to a Make.Linux

Tools/C_mk/Make.Linux

commit d82f70f3320fab59ea36591a92e9e8e39387014a
Author: lijewski <lijewski>
Date:   Mon Mar 29 23:26:46 1999 +0000

    Removed OneFilePerFab option.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 5356b66ba9d1219c921264292a7a6a64576b4592
Author: lijewski <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 6d125b11e8be690303d7c2d6b3caff575ca0ba08
Author: lijewski <lijewski>
Date:   Mon Mar 29 19:27:52 1999 +0000

    Yet another bug fix to CollectNumPts().

Src/C_BaseLib/RunStats.cpp

commit 218078d3758d9801c8be72bf52769a995c2dcd68
Author: lijewski <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 4fa7dc71f662ab3b390079d01e5d0149c8c28dc2
Author: lijewski <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 2e7be105cbcbcce66f9665b0546f965e51f3dc1d
Author: lijewski <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 d7226d499140cad4ad062bac659a17058f8a52ac
Author: marc <marc>
Date:   Mon Mar 22 21:31:27 1999 +0000

    Minor fixups to support ngrow option.

Tools/C_util/ViewMF/viewMF.cpp

commit 68683b458600630f549154fdd74b8a179cc621ac
Author: marc <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 cd5f29bd4f9575e33df876beae49dc862619a0ce
Author: lijewski <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 2b4a8450465da5f09ba087184603c3c8a16df710
Author: marc <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 be34c49bc8d5eca57b70797c7051e3633509b038
Author: lijewski <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 1e541cb66c2d8e708a06aa3d2cd017d5d1316e06
Author: lijewski <lijewski>
Date:   Thu Mar 18 22:12:01 1999 +0000

    Restored clear(int) and remove(int) for Vince.

Src/C_BaseLib/FabArray.H

commit f8fa143e4d275194b1996375ea0df3870ba44612
Author: lijewski <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 694b56c5d0e8bb9f1c2f4c898d38b3d46f4c2cf5
Author: lijewski <lijewski>
Date:   Thu Mar 18 00:13:01 1999 +0000

    Spiffed up message coming from coarsestSmooth().

Src/LinearSolvers/C_CellMG/MultiGrid.cpp

commit 61de2dac228d0502ebc61c7535ded1cfd3f9576d
Author: lijewski <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 4179275be793d1603b19831293a1aee1e21f736f
Author: lijewski <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 d4a44fe981197581b5e2c0c7f860b44a1c4ba929
Author: lijewski <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 969955d800acd0196fea0134cc47eed15e98f46d
Author: lijewski <lijewski>
Date:   Wed Mar 17 21:49:13 1999 +0000

    Fixed bug in dumpReport() regarding wall clock time.

Src/C_BaseLib/RunStats.cpp

commit 30fa6bd9d457717915b14c4812d7613ec18840af
Author: lijewski <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 cefe89cc0f15b21393b69f5277323364d2d6eda7
Author: sstanley <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 525f3eb6152fab19afa846bd9f8cc5a9d63d1614
Author: sstanley <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 f173f7584288d129f9d6a0dd3f3846e8cd423c4f
Author: lijewski <lijewski>
Date:   Fri Mar 12 03:27:07 1999 +0000

    Tab cleanup.

Src/C_BaseLib/test/tFB.cpp
Tests/C_BaseLib/tFB.cpp

commit 76140a22d3159fe3dd9fa1bf3dec0988746d1bab
Author: lijewski <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 0a3a775fd52ef693f2eec61f7b18b21a310198c7
Author: lijewski <lijewski>
Date:   Fri Mar 12 02:55:26 1999 +0000

    Some cleanup and simplification.

Src/C_BaseLib/MultiFab.cpp

commit 887023bc158e574e2fc7421e150976d35c45f7c0
Author: lijewski <lijewski>
Date:   Fri Mar 12 01:09:24 1999 +0000

    Mod for T3E.

Src/C_BaseLib/Utility.cpp

commit 01967220f81a4a98df3caa440f8bcc3ba4060b5a
Author: lijewski <lijewski>
Date:   Thu Mar 11 17:56:58 1999 +0000

    Added Concatenate().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit ee77e1559787d7548040a811a0a087651899fe61
Author: lijewski <lijewski>
Date:   Thu Mar 11 17:56:44 1999 +0000

    Merged in Utility::Concatenate() and some cleanup.

Src/C_AMRLib/Amr.cpp

commit 81f5b2f76c7d102b2dcbd0aaf6fb86af378fb1bf
Author: marc <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 89e5cd7ae52e985453804f847a7c4f662d5b05e7
Author: marc <marc>
Date:   Thu Mar 11 17:48:07 1999 +0000

    Add def for virtual function used by FillPatch

Src/C_AMRLib/AmrLevel.H

commit 0c31984dd875496da9d0655b256fd225eb6f0d83
Author: marc <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 823f997ce3286a8282bcdfa573309d1561f04609
Author: lijewski <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 b75304be901bb57cc989e8ee92ac10e92f9d8f96
Author: almgren <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 9de48ef426f180657cb8fa32a11fe157c0703adc
Author: lijewski <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 6f7bd5b01272d62581dcf8fc5f3b2e5ed9959674
Author: car <car>
Date:   Thu Feb 25 17:35:35 1999 +0000

    re-name again, BOX->Box REAL->Real

Src/C_BaseLib/CoordSys.cpp

commit ee60797c77f7684bf0bf848a6df6237e987e7982
Author: sstanley <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 4b8d65cc540a8f5fbc6b94af3da3b0be91f608f3
Author: car <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 362e341422d27dc6a8850e95e152fa3cacf96908
Author: lijewski <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 5a59d77dca9b74e311f702af0ba726b8951fca19
Author: propp <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 494fcc9c167b30cfe7af228f3e3673190904f717
Author: lijewski <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 0d91bf60f7c29d420f371f27abb2b42abe3e5087
Author: sstanley <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 af628887978b9182880adab0733346970c603a64
Author: lijewski <lijewski>
Date:   Wed Feb 17 21:44:17 1999 +0000

    Added Lp.alternateApplyBC flag.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 0cbaed4792b8ef146f53e27823747ea0af1a532e
Author: lijewski <lijewski>
Date:   Wed Feb 17 00:10:35 1999 +0000

    Explicitly turn off exceptions.

Tools/C_mk/Make.T3E

commit 8a3b6950cf3a7c8dbfc5b6e25330d9816a9f0745
Author: lijewski <lijewski>
Date:   Fri Feb 12 00:07:05 1999 +0000

    +K2 -> +K3 when COMP=KCC

Tools/C_mk/Make.T3E

commit 6a159f8af4b128c851ec486188a5cd225648a21d
Author: marc <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 b90606a24dd6590856431a1c85b1e81000f5be69
Author: marc <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 ea1bc03c8cb1574b7153cea5459159460d644a00
Author: car <car>
Date:   Thu Feb 11 17:07:01 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 734711a54d390191d801b67a3ab1c1897aa30d69
Author: lijewski <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 47a76350d86eda74980eab7a0948868b4b59f51c
Author: lijewski <lijewski>
Date:   Tue Feb 9 21:21:45 1999 +0000

    Little cleanup suggested by Bill.

Src/C_BaseLib/Boolean.H

commit c5038da249d2a34a4c90c74cb58f1a5e6c6e96ec
Author: lijewski <lijewski>
Date:   Mon Feb 8 17:49:37 1999 +0000

    From Matt Bettencourt.

Tools/C_mk/Make.IRIX64

commit 94cc16b39f161ed9ae07b9c2630eb48aea8a0bd0
Author: lijewski <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 79f6b7fb4964962e1462a35c0f1c2d564106a635
Author: lijewski <lijewski>
Date:   Fri Feb 5 18:54:29 1999 +0000

    Forgot to comment out 3rd stuff.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit d996fe516b37965659e428712ef2f7e0feba0562
Author: car <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 6e90c4a9118044343e31acfebe4ee265c1342281
Author: lijewski <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 bb487afefc19e8a9424c6f0e788ad9e728591241
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:56:58 1999 +0000

    Fixed typo.

Src/C_BaseLib/RunStats.cpp

commit 3fa2d1ab600d899a1e41f4509cf9ea57e48eda49
Author: lijewski <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 2dd2cc06b9d1b359c3db082d362acc4d741273d8
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:55:15 1999 +0000

    *** empty log message ***

Src/C_BaseLib/RunStats.cpp

commit f456111737b66d6a7bc1c14f7d271676f7cadd6c
Author: lijewski <lijewski>
Date:   Wed Feb 3 21:48:51 1999 +0000

    Removed RunStats junk.

Src/C_BaseLib/CArena.cpp

commit 86f7180ec2e4b75d1d4127d3b0c155639fa027ed
Author: lijewski <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 e8e66866184262ba9b16a638bf0694edf60e5765
Author: lijewski <lijewski>
Date:   Wed Feb 3 19:29:26 1999 +0000

    Cleaned up checkPoint() a bit.

Src/C_AMRLib/Amr.cpp

commit 03757b3e35d0bc78757054a0e67e7b1db6464389
Author: lijewski <lijewski>
Date:   Wed Feb 3 00:39:25 1999 +0000

    Needed to include <CONSTANTS.H>

Src/LinearSolvers/C_CellMG/LO_2D.F
Src/LinearSolvers/C_CellMG/MG_2D.F

commit e9e385effad4f864681488a799439062455018fb
Author: lijewski <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 02fb3d481c18d2873d4c96012871614d8f0ffac0
Author: lijewski <lijewski>
Date:   Tue Feb 2 23:36:05 1999 +0000

    Removed FORT_SCALADDTO

Src/C_AMRLib/FLUXREG_2D.F

commit 40b07b91037a221a460050d211478902ef381dc0
Author: car <car>
Date:   Tue Feb 2 23:24:41 1999 +0000

    d comment line!

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 13a0118c2453659e63e1d41cf15a7812ab82a5b6
Author: car <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 68a3a4c9acad9717ae71484a5a90edb00807ab12
Author: lijewski <lijewski>
Date:   Tue Feb 2 00:24:03 1999 +0000

    Substituted BL_SPACEDIM for some numbers.

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ff984f2c0434cf61f4f02b699644ba7c376403df
Author: car <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 ba3fe48d16c2bc42eaa892cf28045007440e64ed
Author: lijewski <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 667aeefb5afc52c3e1377c0040120be91f124c15
Author: lijewski <lijewski>
Date:   Fri Jan 29 23:20:25 1999 +0000

    Removed CVS ID string.

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 51238c16f44db1fcc40c49bec00bf7569a26348a
Author: lijewski <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 3539ef7b109b1279a05679206078338c3e7575cb
Author: car <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 7cd5842e691bc3193304d92fefeb570328996574
Author: lijewski <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 f235e554cf4d784972f8159d737303606f8b4546
Author: car <car>
Date:   Fri Jan 29 19:09:56 1999 +0000

    minor changes to quit warnings

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit fca58a949f4cc97fab24f364b83d37371ca55cb2
Author: car <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 30c868a2691b139e77627631c5ce7aa6196a0f0e
Author: car <car>
Date:   Fri Jan 29 17:50:10 1999 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 5a4ebf39ce5f8c00d2e7a959187649757a0259f0
Author: car <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 25aaeee6ed89131a1b01281c09e4ca0649d42e32
Author: car <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 5c1ab54091665fbefb399c0f0bcc6bf39345c370
Author: lijewski <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 b44dfaeb85819105ae93f7aae548cd4239f06e7b
Author: lijewski <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 d7f4937dc68529d99d7fa3d481537cf1a777bd21
Author: lijewski <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 63ceffee61a43cd905218d36464e9252ce2d6627
Author: lijewski <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 387bd56bda65ca05e4f88fe75a89ed86a9c28173
Author: marc <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 c457656985690b796ab5e02e02d56696e822ee72
Author: marc <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 c85010584877c0f7cfc04131aefcb4e67e741589
Author: vince <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 0f76f304e123ee409bcd026abadafc1244f56206
Author: lijewski <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 35fb8644cc6aa10f206f980514fbfa84f50fd7ad
Author: lijewski <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 a3c7c1903a05aa41345436dd99c6d9522aaad531
Author: lijewski <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 54b18d0967f2553047ef9946ab83f813e49ed90d
Author: lijewski <lijewski>
Date:   Wed Jan 20 04:41:36 1999 +0000

    Fixed bug in FillPeriodicBoundary().

Src/C_BaseLib/Geometry.cpp

commit f03b11de5a7057590fc440923c1905e4d3acad33
Author: lijewski <lijewski>
Date:   Fri Jan 15 21:44:22 1999 +0000

    Dealt with periodic nodal quantities in FillPatchIterator::Initialize().

Src/C_AMRLib/AmrLevel.cpp

commit c8f80ae98375f8adc3a94076217fddb00734c897
Author: car <car>
Date:   Thu Jan 14 22:48:47 1999 +0000

    Really old comments

Src/LinearSolvers/C_NodalMG/README
Src/LinearSolvers/C_NodalMG/Rewrite

commit 04f52ff17e52b1dce7faba673ce75ea9b53ec1aa
Author: lijewski <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 33da55ebacde774237048c4b9e0dc63b874e3e18
Author: lijewski <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 a97b92beea6a8eb1fa66ac4915bb7ab58df32945
Author: lijewski <lijewski>
Date:   Tue Jan 12 17:56:46 1999 +0000

    Added RunStats for regrid.

Src/C_AMRLib/Amr.cpp

commit 4ae03dea172561c5b214531b16a5eee6be34f391
Author: lijewski <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 8022608150ae38264505048597c5a9a5ef9e26c9
Author: lijewski <lijewski>
Date:   Wed Jan 6 20:06:56 1999 +0000

    Some cleanup.  Always compile in TagBox stuff.

Src/C_AMRLib/DatasetClient.cpp

commit d6f1dc64f5df91ef61e121813d18d391b8f48e1c
Author: marc <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 fb714bf0ffd67abd1bb417d81a6be6a4dc2d591c
Author: marc <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 b786bb40e5c61f8f0620ee5005656b63464b85cd
Author: marc <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 285d5eda18910017b558204fe634b5e49bee4df5
Author: lijewski <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 1618a426abbdd49a450f4b09f57deb84961da9d0
Author: lijewski <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 e4e6ae8d58c181299c258af49a1fe867d18c0f0d
Author: marc <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 b63527653bd21ee6bd413e1181ca8ca7048b5c0e
Author: marc <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 91df0e74090d0af087548351f540f43679fcb01f
Author: marc <marc>
Date:   Mon Jan 4 18:27:14 1999 +0000

    Add target

Src/C_AMRLib/GNUmakefile

commit a26311bd5cfc0eb4458820ef1191c7ddde7470a3
Author: marc <marc>
Date:   Mon Jan 4 18:26:32 1999 +0000

    Add arg for lib make

Src/LinearSolvers/C_TensorMG/GNUmakefile

commit db67136d13911ade825c1920662a1c8c7729544b
Author: marc <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 3d5365c98e7a3a4b70739723b697d9e7c0f3975a
Author: marc <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 7921275e20a66001e2d36adbe19257aed39db36d
Author: marc <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 ba20383a0a7bfd30955d21c12f4d81c3df0f7b96
Author: marc <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 ac3edde3b3d950b5c70321b96efcc576eee66cdf
Author: marc <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 18ec3315ee07dab34a892b108293eb2d447f90e2
Author: marc <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 0d81b18eada9a15d309d2a3b48c0681106c065b0
Author: lijewski <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 0ac2f5e8f03ea3e373fab87ea006b89d65084779
Author: lijewski <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 661adf8f068b5898eb0c0e7a1dc949c4b5cb6fbf
Author: almgren <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 e933a6aaaca64bcc7b4b861ad59de37ab29a0705
Author: lijewski <lijewski>
Date:   Fri Dec 18 16:47:52 1998 +0000

    Added catenate().

Src/C_BaseLib/BoxList.H

commit 81a2198d1f0d86b4ffbd8946f09dc5f0a4d366ee
Author: wyc <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 64f2231a267fe04b96b5196389db4baff825045a
Author: lijewski <lijewski>
Date:   Wed Dec 16 22:27:39 1998 +0000

    Fixed memory leak.

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 7096ccee2008ef3d0ebcbcb530b2ecf56182f517
Author: car <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 752b122df527af7208af84ac5c4639550d953c9f
Author: car <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 ee0c9beaa576fe469d683b3622fcb5c02e14ef3b
Author: car <car>
Date:   Wed Dec 16 18:42:53 1998 +0000

    test infrastructure

Src/LinearSolvers/C_NodalMG/inputs
Src/LinearSolvers/C_NodalMG/proj.cpp

commit be6d5d1a0fc4a5fd66b9a6338ffba9338120aefa
Author: car <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 f92e68da5345f17ad442958e22dacb3f783b522a
Author: car <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 b408b79a1f762a10a9bf56586eee91d30a0365a2
Author: car <car>
Date:   Tue Dec 15 23:34:56 1998 +0000

    more checking options

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 33fab28dc32f79b1b9255bca4007286da63caedd
Author: lijewski <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 a93bca36bcd6a4173468177089fd12cabfac02fc
Author: lijewski <lijewski>
Date:   Tue Dec 15 18:13:24 1998 +0000

    Had a bug in task_list::execute().

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 55f79ce7f039fbb5aa43377bdfdcd8315b166ba2
Author: lijewski <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 e89b39ab210640da51a120bb8362e119255248a5
Author: lijewski <lijewski>
Date:   Tue Dec 15 17:22:47 1998 +0000

    An improvement to task_list::execute() loop.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit b98e9caf68b013743f947e16b75739f7c98a0797
Author: car <car>
Date:   Tue Dec 15 17:01:30 1998 +0000

    better execute loop

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 28421c74cc83dabbae74a80ad1723a456446e13b
Author: car <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 81d772f6311a06bca814a02510a13a678a1bb5af
Author: lijewski <lijewski>
Date:   Mon Dec 14 22:43:11 1998 +0000

    Integrated in <REAL.H> and <CONSTANTS.H>.

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 75a348803a50352bf77f29930d4092e4750c0895
Author: lijewski <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 01f9c2795efb946bb636af81b17208671aabb340
Author: car <car>
Date:   Sun Dec 13 01:21:38 1998 +0000

    sleep flag

Src/LinearSolvers/C_NodalMG/proj.cpp

commit cedeb6981f552afca3ea8ac5ab182c0c2dac45f3
Author: car <car>
Date:   Fri Dec 11 21:55:40 1998 +0000

    T3E KCC change

Src/C_BaseLib/Utility.cpp
Tools/C_mk/Make.T3E

commit cdfaaa1ba1c6c59c004d4084601338776386c57a
Author: car <car>
Date:   Fri Dec 11 21:54:25 1998 +0000

    T3E change in prototype for _rtc

Src/C_BaseLib/Utility.cpp

commit 08bb9e6fd43088843fc60d7db1a88db2761c80d4
Author: car <car>
Date:   Fri Dec 11 19:21:26 1998 +0000

    fix for rwtime == 0

Src/C_BaseLib/RunStats.cpp

commit 343c629dec8627b3e996768014547794039cf7ca
Author: car <car>
Date:   Fri Dec 11 18:55:32 1998 +0000

    added inputs file

Src/LinearSolvers/C_NodalMG/inputs

commit bd3a90c0be4d1eca8be2c5244bd97ba7e7329d07
Author: car <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 452f7c05c7865c9c2651eecd9345d6734d0f753f
Author: car <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 d623e0b55d6d1f00f57f349c32b0025245f6415f
Author: lijewski <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 476926dfa78561842541463d7351b4edde958e03
Author: lijewski <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 c92be1e9df16ae88c1d0786fe324f357f25a6f33
Author: car <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 3bc6f5fdf06f3368768ca435cea389c6ad24bd5b
Author: car <car>
Date:   Fri Dec 11 00:01:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit a4364e6b2daf5aa07edd87d9034cad5025cbb948
Author: lijewski <lijewski>
Date:   Thu Dec 10 23:34:58 1998 +0000

    Added FillFabPlus().

Src/C_BaseLib/FabArray.H

commit 7134b731d184ef98b880f47e0fde111d9c793fa1
Author: lijewski <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 d943a9da8c8856a09d83f39767324e8bdf0cfd68
Author: lijewski <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 426ec31f940efa3d63b0355e05f7b0821e4cb867
Author: car <car>
Date:   Thu Dec 10 23:16:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 059600064f10d8b819308879c37a184a17e74794
Author: car <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 14923aafea7b18da8f307f0b0b71d1fafc7d0d1f
Author: car <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 55125e31ed5be1b7a69335439633d59e002fc8c0
Author: lijewski <lijewski>
Date:   Thu Dec 10 22:16:07 1998 +0000

    Changes to buildPIRMMap() for nodal MultiFabs.

Src/C_BaseLib/Geometry.cpp

commit 6226ebdaa2c5f67aa4cc4c2654c7cf4b4b16accf
Author: car <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 c1624e71c57b266cc62f9277f137a5ae0bee94b1
Author: car <car>
Date:   Thu Dec 10 18:41:21 1998 +0000

    remove extraneous dependency check

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 4d29e1de51d21248209a347394855e8664105218
Author: car <car>
Date:   Thu Dec 10 01:02:38 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 961c8d80d3864d63361fb6126d123017fa9113b8
Author: car <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 99f8a0997759824ffe4f6164031e101b804cadf8
Author: car <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 f6d04474e01c8d1a2f8356603672c28587989ba1
Author: wyc <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 740ab6953b5858070cf1c3b3c2f3da9e326e3819
Author: lijewski <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 73f6df42166b2b1539d99dce2b7f49666daf3629
Author: wyc <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 72612ac1e291535d7336cbc271e8eb7985ba8e7f
Author: lijewski <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 f3d3064190aac34955af49fa27b912624e46e0d5
Author: lijewski <lijewski>
Date:   Mon Dec 7 18:39:21 1998 +0000

    Mods to compile on T3E.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 20ea7b14dfeb2dd1710a5276887d574203cb732d
Author: almgren <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 4f72d3f8cfcd102a98d46629cc63930357f49111
Author: car <car>
Date:   Fri Dec 4 21:32:48 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 9cd6eaeca22dcc6dc51dbd1d973ebe5cacab39b6
Author: car <car>
Date:   Fri Dec 4 21:19:31 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit fa8ee8d315029adfb85e87d1e8a084e84f68a8e3
Author: lijewski <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 dcda95e59a6cda0c841b654d13fcb45c777d1198
Author: lijewski <lijewski>
Date:   Wed Dec 2 18:36:45 1998 +0000

    Removed bad assert().

Src/C_AMRLib/AmrLevel.cpp

commit 6b3ba309e1847503b5ee5cee986131a6e994a7ce
Author: lijewski <lijewski>
Date:   Wed Dec 2 17:52:55 1998 +0000

    Fixed another periodic bug in FillPatchIterator.

Src/C_AMRLib/AmrLevel.cpp

commit 0e30b5db293b7d19e741d813fd58d8c77ae9e54f
Author: car <car>
Date:   Wed Dec 2 05:58:57 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 2ff5274c6c8ee320f66568ad3c22b2c27ef4f18c
Author: lijewski <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 ccca50c5406553eea50df2607e6b2706addee1dd
Author: lijewski <lijewski>
Date:   Wed Dec 2 00:04:06 1998 +0000

    A tad cleanup.

Src/C_BaseLib/GNUmakefile

commit 4fc12c17bd04416c63d32d3d55a916a3fb8a27a0
Author: lijewski <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 f56bee7d41171cbb980ac12e2b8330bae471b256
Author: lijewski <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 31cfa49f6f9edaed451ce263639c4359d2422dd5
Author: lijewski <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 ce24534953f4b6bb7d23953f9011c0805c004c46
Author: lijewski <lijewski>
Date:   Mon Nov 30 21:13:38 1998 +0000

    Mod to get to run on T3E.

Src/C_AMRLib/StationData.cpp

commit e4f52aea3a3bda81a054fe896f9db30d15dfe803
Author: lijewski <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 2156eddaaf1b6fabb6b993815b56c02d5e49ddfd
Author: lijewski <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 16eea903622c4767ac209a6edbdd71b63eb342f5
Author: lijewski <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 f9c419d0f368953a092b133a2f5fe9a0d04b6d91
Author: lijewski <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 ed4305ec133bf7c1d00086f00d166f7569bceb13
Author: lijewski <lijewski>
Date:   Sun Nov 29 00:22:09 1998 +0000

    Added some const versions of member functions.

Src/C_AMRLib/AmrLevel.H

commit 86a530e08ec906f668f1673c32c2081f2c8e4596
Author: lijewski <lijewski>
Date:   Sun Nov 29 00:21:41 1998 +0000

    Looking pretty good ...

Src/C_AMRLib/StationData.H
Src/C_AMRLib/StationData.cpp

commit 09764f57bb4bee464e300082dcace0f0476ac2bb
Author: lijewski <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 c8f7a23b8880782d11fa308d10ac60ab72bde862
Author: car <car>
Date:   Thu Nov 26 20:30:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1fec37eac74c676c84414960ce5be1b4f9cf05ec
Author: lijewski <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 16b902920f8a239c15aafe8aa5b45a97a0461ea1
Author: car <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 1fa5d5196f335092c8a06b1bf8cde2d4a0f6a592
Author: lijewski <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 4eb687baa573803736f65fd21c9e2f1d82f13c13
Author: wyc <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 fcf009fe889ec30a85694e1de43970949e945409
Author: lijewski <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 0ef188efe02c12f4516bb888e1d298eefb467135
Author: lijewski <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 034b6f01dd9fae10396d7dac9b3f8ecc89c0e74c
Author: lijewski <lijewski>
Date:   Tue Nov 24 01:01:14 1998 +0000

    Merged in new Reduce() functions.

Src/C_AMRLib/Amr.cpp

commit 070ac872c42ad2a0bced22bab810ae20dbce654e
Author: lijewski <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 817b9bd43156533113830742231c41c63c1b8a09
Author: lijewski <lijewski>
Date:   Mon Nov 23 22:39:26 1998 +0000

    Added const versions of newData() and oldData().

Src/C_AMRLib/StateData.H

commit d1e7556f10b703106a5e973a4d2edd08265f3ee2
Author: lijewski <lijewski>
Date:   Mon Nov 23 18:27:01 1998 +0000

    Removed canned procedure.  Was proving too much trouble.

Tools/C_mk/Make.rules

commit dbe17c897916dbd5e1a9c6fe21ec50aff0acf444
Author: lijewski <lijewski>
Date:   Mon Nov 23 17:56:42 1998 +0000

    Fix for busted gmake on T3E.

Tools/C_mk/Make.rules

commit 73c74592599f7b6fbc47d04225e4c9c2d6cf7e3e
Author: car <car>
Date:   Mon Nov 23 17:31:36 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit 4ed2b516d2b9f666704b75f9c4bff3e8ccd9eb8b
Author: car <car>
Date:   Mon Nov 23 00:50:23 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit cb1e08598a66a755d58238b104115e953f8e9673
Author: lijewski <lijewski>
Date:   Sun Nov 22 17:42:54 1998 +0000

    Wrapped the closelib junk into a canned procedure.

Tools/C_mk/Make.rules

commit 7e616ec0198a19ecb0fed2aa044a65680e196eae
Author: lijewski <lijewski>
Date:   Sat Nov 21 19:34:19 1998 +0000

    Added ti_files directory for cleaning.

Tools/C_mk/Make.rules

commit 50b8e9ffa494a6a4a9e79c3f6e9e9731923a00e3
Author: lijewski <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 544dd78890e62e33e6d4960651069ecb77700711
Author: lijewski <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 94ff98a06cf456df1075828263d71073c925e15d
Author: lijewski <lijewski>
Date:   Sat Nov 21 02:49:39 1998 +0000

    Simplified the library closure junk.

Tools/C_mk/Make.rules

commit 48452fc953f89c267b8f9c3b0fa8bd1de2c37e1e
Author: lijewski <lijewski>
Date:   Sat Nov 21 00:27:43 1998 +0000

    Yet more OUTPUT_OPTION mods.

Tools/C_mk/Make.defs

commit 8dd7468e4493a0f4fb43cbf6d81d15f18ae95e59
Author: lijewski <lijewski>
Date:   Sat Nov 21 00:24:14 1998 +0000

    Bug fix to form of *LIB_OUTPUT_OPTION.

Tools/C_mk/Make.defs

commit f77afe0060da3e89d642997d266c7b95f5040b8f
Author: lijewski <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 5974512f34a2f81f92c6719f3544c1efe6c87239
Author: lijewski <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 3c32b18940e630726e8df21ea6ef774068a37b1c
Author: lijewski <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 7d4aa028c32bb9d71bc8c0c1808deaa3958efdca
Author: car <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 ce8d5081f10fcba310cc10909e371e4baeeb1455
Author: lijewski <lijewski>
Date:   Fri Nov 20 21:23:36 1998 +0000

    ld -> d on an sprintf() call

Src/C_BaseLib/VisMF.cpp

commit 9d6a2b758f10be36cfbb28254df90b7627b2bcfd
Author: car <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 2d15c0173554e757eee17ffed048b710191dc2b3
Author: car <car>
Date:   Fri Nov 20 20:29:45 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 8ec28562b53e6460f70ec3183825547b01495620
Author: car <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 f577d3f16febad5c1787df31b7c99579920e2e7b
Author: car <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 9975e0df32088945b7ef5dcd18d0c7acf2685209
Author: car <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 49db930eb54de4a8b84c531ce5bd7e9d6682a559
Author: car <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 302677eb22eb4fb47e3795d36aaf3d1672fa817e
Author: car <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 447f168cdc7a593a0d373a79ae08e947db747e77
Author: car <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 88a27b71bd3941d4fd7cf419198325db33d600ff
Author: car <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 6db0e8287b333ea32d8df747049582c9818487c8
Author: car <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 551df3472d3e69f0a0a3c7302d3f7a0ab41cfded
Author: car <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 939ad0b8848b5b971d0fec8d46935e87548729c0
Author: car <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 1dd96aedde70d36b4d1161fa40c98b41c751af04
Author: car <car>
Date:   Wed Nov 18 21:08:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ea3b10dbb4389f401497d48357cb1af1fee2d9d9
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:47:05 1998 +0000

    Updated to reflect new Make.defs.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit f9749fe12241779480b6da942549256d32afb516
Author: car <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 d8992c7c8622a10bbb4d8ab3e6e9348551a9f6da
Author: lijewski <lijewski>
Date:   Wed Nov 18 20:34:50 1998 +0000

    Updated to reflect MPI in machineSuffix.

Src/LinearSolvers/C_TensorMG/GNUmakefile

commit f3894c0aea05057e29998c1ca821e1038fa8c7da
Author: lijewski <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 886736fb8cbd2d00c91abccb3022f2e5f18a7c61
Author: lijewski <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 403fa1ce963b268db579b5845e9f8c2dcb818451
Author: lijewski <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 f9e647742040d5f611e6330023c0084b42f64973
Author: car <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 5e5304efb17d7b7149ee55da6fa2242930b7dccf
Author: car <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 55e2d77d851f186f79eebdedce9890b5b3b6aaa9
Author: car <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 aa61f39ebe8767f9af24acd7bcceb8401dd0ae14
Author: car <car>
Date:   Wed Nov 18 01:30:51 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit c715b4a404c5594bf37ee75e2ed8db634ce9f401
Author: car <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 201970be052024a0c639e99e8c08488e57793eb6
Author: car <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 35e209c9ccb2b20dac9e1df5020c69ebee4363d2
Author: lijewski <lijewski>
Date:   Tue Nov 17 19:15:39 1998 +0000

    Small touchup.

Src/LinearSolvers/C_TensorMG/MCLinOp.cpp

commit ed22fe92ffb33576101f74d7a881246cf293ac18
Author: lijewski <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 8a4e999d9684460fb61b99ea6bb2a21701f218d7
Author: car <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 3d156a47245d44ab5154705a7efabbdc9b411e04
Author: car <car>
Date:   Tue Nov 17 17:48:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 146faefe9823616eeb99ba430418491b2cc8a53e
Author: car <car>
Date:   Tue Nov 17 00:51:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit dbce7d325c1ca0eec06011678f2fce72688e7f2b
Author: car <car>
Date:   Tue Nov 17 00:48:50 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 2820cb5a3fa81b20c3d04154c08afc68a130bd4b
Author: car <car>
Date:   Tue Nov 17 00:38:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 5a52bf2ea58f5894908c09bf3a8bb34228f5310f
Author: car <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 7e4f5bd1f2e44ca1343a9b96ebe8f1d05c163ebd
Author: car <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 c219930a6d8ad2b1f644d95c987cc923ff603200
Author: car <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 855ba6e164ece01b106cecdb60fc70f6c62f6798
Author: car <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 d614cd22c4da61d595d6aadbf2abfdec43ae7f23
Author: car <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 d4daf18e8c0392679a203541011344adc9cfdd26
Author: car <car>
Date:   Mon Nov 16 18:11:49 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit fab3cce418eb22ff022fbd95104b363f897d5bbf
Author: car <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 75bcd00d45cf2134e76ef494cc7a92d63afcd935
Author: car <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 200f3394c1b0570dae3f41037503c51a308d0863
Author: car <car>
Date:   Mon Nov 16 15:53:17 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2f30e89dc2d772c6db4d9ed3429cfd5d5d912b94
Author: car <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 e4cc952417abcfc1985c3ad907bdc071482e55d7
Author: car <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 e488e7ffbfb0aa28cf44cc70598c9df4fa131ff8
Author: car <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 b3c3d6dfa05754297f8e14564a23086ddb47bc98
Author: car <car>
Date:   Sun Nov 15 00:01:27 1998 +0000

    win32 support

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 26bf1132774b740f936cd035b2a6f834ba64514d
Author: car <car>
Date:   Sat Nov 14 19:38:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 121fc22589b71cc0b68607026a34c612107f99bd
Author: car <car>
Date:   Sat Nov 14 00:34:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit cdaa86c34d295bbcf736f74b80a326c40fa12971
Author: car <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 2c13a0bfc7ac08f70bc4b885fa4d7ce39aee7116
Author: car <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 7c3b71fc168e23527ee70309c885facaae8a12a1
Author: car <car>
Date:   Fri Nov 13 20:09:28 1998 +0000

    Temp file name.

Src/LinearSolvers/C_NodalMG/.cvsignore

commit ef9948b061f008c9e9e865f6507aafb872462fa4
Author: car <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 9ddae75afabf11a9b2ad495a86400632fc1c1b24
Author: car <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 922cf0a2d9af33988cc6542c0c53808bb5482a22
Author: car <car>
Date:   Fri Nov 13 16:03:51 1998 +0000

    EBASE should be null

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 5b7e7bd2e95a2769a4ad696bb3e9eddb638bfcc9
Author: car <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 f44f6033e44f9aceaa195869c25c0539ce40c1af
Author: car <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 ed4b454cf58c8e3a3d2c86087a5145b3cefc74a2
Author: marc <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 bf18f8ae1d80dc1ca5e4b546f4ccff5968437cad
Author: car <car>
Date:   Tue Nov 10 02:21:59 1998 +0000

    libs target

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 19086d0b786f91aa58f38cb54122af23e99bac89
Author: car <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 0b3d5ac6ef8a6eba182dc62dedc9efccd0bef466
Author: car <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 dcf254c4acc8074c36be7cab1ddaaf0766ea24c8
Author: car <car>
Date:   Sat Nov 7 21:34:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 1906d0a7c8492c12a792dd5a7e69a4768c4f7b76
Author: car <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 df4207780b774f99bc8c2fedac57b43ff7acdd3c
Author: lijewski <lijewski>
Date:   Sat Nov 7 02:51:08 1998 +0000

    Updated to reflect FillPeriodicBoundary() mod.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 32dbe815c2ab692301d18bd28826f1250684c72f
Author: marc <marc>
Date:   Sat Nov 7 01:45:11 1998 +0000

    Remove indenting whitespace.  Uglier f77 generated, but guaranteed correct

Tools/C_scripts/strip72

commit bead7c2cbc7f6ff1fc0026b643545f67de160a6f
Author: marc <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 98aeb836a9fd7c067280d30aeae6ae0c1a5c6e61
Author: lijewski <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 c2f004193905ad211f47a5667869720ad1224ba0
Author: lijewski <lijewski>
Date:   Sat Nov 7 00:30:43 1998 +0000

    Mods for FillPeriodicBoundary().

Src/C_BaseLib/MultiFab.H

commit 00423c5a794702277e7fddc5ee7e3872c404b1cb
Author: car <car>
Date:   Fri Nov 6 21:35:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/RegType.H

commit 88137956ff1f2c2d6e1491163929ee5bcfd9943c
Author: car <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 e0943b3adeca0fb1466e1d265d91767a99fa2b46
Author: car <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 af91c0be23d01e95250d0df9898b1c7aa75ebcb9
Author: car <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 18b5c57cdc2d7de6bbf32fa7a273eb606b657a0a
Author: almgren <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 946f44e2d868a4f8fdde3a13c4735212e06718e8
Author: almgren <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 67e5f5134cfad193953cb09432f9bf240184e8b7
Author: lijewski <lijewski>
Date:   Wed Nov 4 00:45:16 1998 +0000

    Added DataLog() ...

Src/C_AMRLib/Amr.H

commit 0302d3f164260b7e07f011459cde6f81e4ba8505
Author: marc <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 da8bfdf9524001f7eee861e79ade076886e2114f
Author: almgren <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 a2e16ae83686c7cf618b726a8bc77b6c9bd5f163
Author: lijewski <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 a4bb32c2898c792f75df11afbc22b64b1e182307
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:35:55 1998 +0000

    HG_DEBUG is defined only when building executable.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 77815d491376c8f311e06385fe083d4ddb89ae7f
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:19:48 1998 +0000

    Added PROB_AMR_F.H

Src/C_AMRLib/Make.package

commit 985caaf4125d68508fe6701e05b533d2283ed57d
Author: lijewski <lijewski>
Date:   Mon Nov 2 18:16:13 1998 +0000

    Forgot about amr_defs.H

Src/LinearSolvers/C_NodalMG/Make.package

commit cfe4a4d409274b1e947b000b58eb4e7ccfcd05f0
Author: lijewski <lijewski>
Date:   Mon Nov 2 17:13:25 1998 +0000

    Added LevelBld.H.

Src/C_AMRLib/Make.package

commit 1c011c778cbcd97a6f81e0aa610e431104ead0c2
Author: lijewski <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 52278f5cf706e59f410b95371e124dd7b11ab232
Author: lijewski <lijewski>
Date:   Thu Oct 29 21:56:56 1998 +0000

    Fixup for doc++ DVI generation.

Src/C_BaseLib/VisMF.H

commit 9a827884baac6f0775e404075918ea00b18449a8
Author: car <car>
Date:   Thu Oct 29 21:56:26 1998 +0000

    *** empty log message ***

Tools/C_mk/Make.defs

commit 30c073d37302988cc85f9f3bd10f9453b312ed52
Author: lijewski <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 273fc3b441d7e94b3075e21a35a072aa36298b79
Author: lijewski <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 99c494d38907ca3b3b614f7c2470d9d9e25c1afc
Author: lijewski <lijewski>
Date:   Thu Oct 29 16:33:39 1998 +0000

    Simplified decision regarding how to set QNAN.

Src/C_BaseLib/FArrayBox.cpp

commit 11708f857fccc2656f76d021bae1a73051fef47a
Author: lijewski <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 ba6f1b98bcfceccc4757ecffa3471baf328f6d60
Author: lijewski <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 3061cb551149b02adfe4095a4a9b9e85a582ed7f
Author: lijewski <lijewski>
Date:   Wed Oct 28 22:01:15 1998 +0000

    Forgot BC_TYPES.H

Src/C_AMRLib/Make.package

commit 5f143673aa3370829e96de6b87d2128df0917cbc
Author: car <car>
Date:   Wed Oct 28 18:43:04 1998 +0000

    __GNUC__

Src/C_BaseLib/FArrayBox.cpp

commit 52b0460e5803173a36caaedc2af8ea892a98ff3f
Author: lijewski <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 2287f5a6d1c3406d7f9d85f907c4f4afa7cbf45a
Author: lijewski <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 abb47a3f1bc4659b2022c42d93603ae29f7857f6
Author: lijewski <lijewski>
Date:   Wed Oct 28 17:42:16 1998 +0000

    More work on building and installing library.

Src/C_BaseLib/GNUmakefile

commit ba216e5528abcf02421545b7be6460ecc9724d35
Author: marc <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 d9e3e91646ecf94dbf1830faaaa3e8cbace87f7a
Author: lijewski <lijewski>
Date:   Tue Oct 27 22:07:10 1998 +0000

    Redid previous fix in a slightly clearer way.

Src/C_BaseLib/FabArray.H

commit aac37fb48793a9722cbd019e4007a013875a8e56
Author: lijewski <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 b0bfc84172e5e516f2d85af4d2af429275554e5f
Author: almgren <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 5b5fc73d0b999182579198aebae6f8dbe51c871a
Author: lijewski <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 a5961cde157f40192b945a094c975aac141e008c
Author: lijewski <lijewski>
Date:   Mon Oct 26 23:58:50 1998 +0000

    __GNUC -> __GNUC__

Src/C_BaseLib/FArrayBox.cpp

commit 4366b688a14db282fac170e61a79254bc1124104
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:51:38 1998 +0000

    mpi_waitall -> mpi_wait for RunStats.

Src/C_AMRLib/FluxRegister.cpp

commit 633b7c9c85853ec295e29ad8daa782c2507ef5ae
Author: lijewski <lijewski>
Date:   Mon Oct 26 20:51:15 1998 +0000

    Optimized MPI communication in copy().

Src/C_BaseLib/FabArray.H

commit 39ebb17ec26519512149e89e77b81ce72050e570
Author: lijewski <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 9717a6dbf4a04326a581e8eb91f1f9dabcaba6f2
Author: lijewski <lijewski>
Date:   Sat Oct 24 22:26:42 1998 +0000

    Figured out the bug in 1.49 -- Yes!

Src/C_AMRLib/FluxRegister.cpp

commit 7953ce0a46b483118c6d2692bee21e48b22b65d5
Author: lijewski <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 22feb3137276d6b665c68aefa407df9ec057899b
Author: lijewski <lijewski>
Date:   Sat Oct 24 16:49:25 1998 +0000

    Optimized communication in CrseInitFinish().

Src/C_AMRLib/FluxRegister.cpp

commit 7674180b05ae882ec555890cec7cdb4faf42fdce
Author: car <car>
Date:   Fri Oct 23 23:46:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit f08bcca8aa92e71005192c0c2d59f2bcd4c2417d
Author: lijewski <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 75e636653172ebaf9826b84135f04bc2488906fd
Author: lijewski <lijewski>
Date:   Fri Oct 23 01:59:35 1998 +0000

    Added immediate return in CollectData() if NProcs() == 1.

Src/C_BaseLib/FabArray.H

commit 4a0659761fdee5a021fc8723460b7cb8dc148390
Author: lijewski <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 cee51ace7cd1b3c3d9161ac4d41158d82b42f3b8
Author: lijewski <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 650e23337104bc82cdd1e846ac9eef8c707211de
Author: lijewski <lijewski>
Date:   Sun Oct 18 01:44:17 1998 +0000

    Added new cut at CollectData() minimizing # of communications.

Src/C_BaseLib/FabArray.H

commit ecf60026bf8029db9b2ab5250027895fefbd13a5
Author: lijewski <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 1d158ca48899b6fc2176a31754e61f7684ccb8bd
Author: lijewski <lijewski>
Date:   Thu Oct 15 21:53:02 1998 +0000

    Now cache the AddBox() info in the CopyDescriptor.

Src/C_BaseLib/Geometry.cpp

commit 80989c21a2c9997223bdf0dd7746e90676d43ffa
Author: lijewski <lijewski>
Date:   Thu Oct 15 21:52:40 1998 +0000

    Now cache the AddBox() gunk in the CopyDescriptor.

Src/C_BaseLib/MultiFab.cpp

commit 0211f4f7640923e1d42fd0d43f8e0505a4775d68
Author: lijewski <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 25e70fb0cad58a31effe9d9a5e1f123e747d9d14
Author: lijewski <lijewski>
Date:   Thu Oct 15 17:14:32 1998 +0000

    Added instrumentation code.

Src/C_BaseLib/FabArray.H

commit 7902f0d1fdd3ba604e195c8a44bb7812dc3fd302
Author: car <car>
Date:   Tue Oct 13 18:20:32 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit f2c6765639833f2c61f405e037f26e00b947e442
Author: car <car>
Date:   Tue Oct 13 18:19:34 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 1a3b44f5340774d6a9448bed899c9f8f6d041640
Author: sstanley <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 d3cc009312f42acfbea0fa8d2522286e5a8338c5
Author: car <car>
Date:   Thu Oct 8 20:23:57 1998 +0000

    minor refinement of message

Src/C_BaseLib/BoxLib.cpp

commit bf2a48a9bf1a0bd0e4d8bfe6232d050bc3f2cf9a
Author: car <car>
Date:   Thu Oct 8 18:19:42 1998 +0000

    oops

Src/C_BaseLib/BoxLib.cpp

commit de8ca3e63e9ae8c31d27ffee235c1660c411d09b
Author: car <car>
Date:   Thu Oct 8 18:05:45 1998 +0000

    id string for abort/error

Src/C_BaseLib/BoxLib.cpp

commit fbe24966640f4fef23ebf4e5ede7e7b434910499
Author: vince <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 0f855d3507e9e08726ce1e8ac6162ffef979995f
Author: vince <vince>
Date:   Wed Oct 7 20:51:59 1998 +0000

    Added Make.AIX for blue.

Tools/C_mk/Make.AIX

commit 16b6440841387b7187583b20c136dbd5fbc19822
Author: lijewski <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 751906b9cd5d5408df8a1473c081b2c1c79434f1
Author: lijewski <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 a7b9886bd51fc1631b1260b1d5855802fc3ad1ca
Author: lijewski <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 9273d7d44c38e118010f48611145c5be01cff434
Author: car <car>
Date:   Tue Oct 6 20:11:01 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 41f8e3383f33447905d95a324f13aa1c71c35017
Author: lijewski <lijewski>
Date:   Fri Oct 2 19:36:48 1998 +0000

    Relaxed a couple assert()s in copy()

Src/C_BaseLib/BaseFab.H

commit 8ee3c335080582f4337e19f2d9cfa60e5b7258d9
Author: car <car>
Date:   Fri Oct 2 18:42:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 608f2614a6001eb331a0c8f3bb7d872180a3a590
Author: car <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 706195614ed9d963f7c8a1d95e5898449b266cb4
Author: lijewski <lijewski>
Date:   Wed Sep 30 20:07:18 1998 +0000

    Added tad more useful error output for bldTable().

Src/C_BaseLib/ParmParse.cpp

commit 89643e1933e7a87a259c64ed22a78a1b2453b509
Author: lijewski <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 157241cb30e13e1e23efed18fde719217659608c
Author: lijewski <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 527b7ae09575d76b767808334221ed915309d6cc
Author: lijewski <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 568a0d5cf5befbd5d68ac3c196c74d780105958f
Author: lijewski <lijewski>
Date:   Tue Sep 29 20:08:27 1998 +0000

    Added copyright macro.

Src/C_AMRLib/DatasetClient.cpp

commit d6999623cc1ebed83a5ec1eab40567cbe5afadd2
Author: car <car>
Date:   Tue Sep 29 18:05:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 385bc52345be13819da1c849295c91dadad12f0a
Author: car <car>
Date:   Fri Sep 25 23:00:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit f4ed19d4460349ac24f67146f282e336e790235f
Author: lijewski <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 b52c7d3befe04273b88897afd1cd8d16030e49ec
Author: car <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 2c6e0d158d9256bfbd66731d97589c66dea0248a
Author: lijewski <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 ec195f309cc92eecce4cc52412310a7a4db83863
Author: lijewski <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 bd3839d5c8232b2e792a72c271ef4d9e9bdc32ef
Author: lijewski <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 734a2318e50a581578596eaa436cd3c8e68afa1d
Author: car <car>
Date:   Tue Sep 22 20:29:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 710021567886544cc673812d4b99f52ae13cff71
Author: car <car>
Date:   Tue Sep 22 18:06:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit be35caf639e93ec17646bc70e0ecc8916dc60496
Author: car <car>
Date:   Fri Sep 18 20:26:12 1998 +0000

    proj.cpp

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 9e7e421614024e3afc00485723e095bd513e64cc
Author: car <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 db6788cc56eb184e6702e8e66ded4af9b11d95cc
Author: car <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 db7d37acb2a5e983cfa7512d36d8da59ea7d7dab
Author: car <car>
Date:   Thu Sep 17 17:05:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 2d94c7ecf8ee39531847b0f553caadf4103b20e5
Author: car <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 4418bb1175f9d2bd2e0b552350e0e21f8c4939f4
Author: car <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 47c0da5e9155b149fdd28f6c376530d92a38b0c3
Author: car <car>
Date:   Wed Sep 16 03:36:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 2329a2e804320ca3b13ca306a60c235f9fd7a730
Author: lijewski <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 da893f7ec4c65231499debfd1c1bde9c0bbf4ac9
Author: lijewski <lijewski>
Date:   Tue Sep 15 00:11:06 1998 +0000

    Undid 1.20.

Src/C_AMRLib/StateData.cpp

commit 639ed6b3264abf7849b00c5e5cf89d97e9362278
Author: lijewski <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 40e1430ca7e72c4da435a3b8bbeda375f8550b56
Author: lijewski <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 5c996ae3cfafab438523901f4d292cd9022ddcec
Author: lijewski <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 24e8f374c12bbca71d98a7c77807c146abcb6efb
Author: lijewski <lijewski>
Date:   Mon Sep 14 21:49:56 1998 +0000

    checkPoint() always used fab.format=NATIVE

Src/C_AMRLib/Amr.cpp

commit f38c2f511f9c3fd8677974e2cc0f14c8f8f61e92
Author: car <car>
Date:   Fri Sep 11 21:15:42 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit bb60f21f571e36cc9a7d52b7dd1bc914379e6146
Author: lijewski <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 d9c2a723e7b3e3788c8c742a33495c92d69f7daf
Author: lijewski <lijewski>
Date:   Fri Sep 11 19:58:15 1998 +0000

    Minor cleanup to linInterp stuff.

Src/C_AMRLib/StateData.cpp

commit 923cfd6a71957e6068ef1b84ee530a62a1959076
Author: lijewski <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 f012b4f26632a6eea623d6ac84f3465287756a77
Author: car <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 9aacfb93dd2687dd9695c108cb69bbe3c0db3662
Author: car <car>
Date:   Wed Sep 9 19:57:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 3ed433555c6e3fdcaf1b2365f1eb906f7a00a2fe
Author: car <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 45cf93d29364c41f5c55df12b0f7e3e3c0c0d950
Author: car <car>
Date:   Tue Sep 8 23:12:15 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hglib.dsp

commit 2b5620225cef07a946c57b847ba64b416f8113ab
Author: car <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 90eb70b66b3de157095e03734f4543a4423e8663
Author: car <car>
Date:   Tue Sep 8 23:00:04 1998 +0000

    *** empty log message ***

Src/C_BaseLib/pBoxLib_2.dsp

commit 57cdd7b13035302d505ed24cad4f7c06443b6e4b
Author: car <car>
Date:   Tue Sep 8 22:59:40 1998 +0000

    cleanup

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit d6331628bc751ea0cafab9f8b235038123b4545a
Author: car <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 ce05e0a9949fdf04b2a3e679b73eec41dc79cad4
Author: car <car>
Date:   Tue Sep 8 21:07:32 1998 +0000

    counted pointer

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 4d254df0da070078dcad99ce1053944eb887c79c
Author: car <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 4aef54aa70c7acb1b9bf8b3c5433911eb1b16686
Author: car <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 8e6bff33f49f788ea4dec30c87c6727be4d753d0
Author: car <car>
Date:   Thu Sep 3 18:30:15 1998 +0000

    Really No changes.

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit a2c4039db8020fe224960dc83e4fab1ed57f24f8
Author: car <car>
Date:   Wed Aug 26 17:48:15 1998 +0000

    added back graph stuff

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 3aeba57bb0280faf4bc23fc4898d4dc309ec0e04
Author: car <car>
Date:   Tue Aug 25 23:44:25 1998 +0000

    added some more temporary files to .cvsignore

Src/LinearSolvers/C_NodalMG/.cvsignore

commit 0185cf4a5dbfe837b5d45be726aebdf1d5daa70e
Author: car <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 3c07f96043e4dc3da790ffe34b7c96e36e79b886
Author: car <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 b47a9df5fae0525533e1dfa0816e9312c71e8751
Author: car <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 aea58ba4e6216a784b3f0c6247d4a6216b091b7d
Author: car <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 d5ecf2650057e5bf842a92e3f76dd4c3677b3000
Author: car <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 e6d5edcad64aca2642f08a437a76fff584e20939
Author: car <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 4f4a57f7d6c65d37c7119b9794a90139c8b180a1
Author: car <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 9c1c1c289ee4c6b82dec03eb975c2dd2a923fa8b
Author: car <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 ce7bdb0054dcf472af9df3716420791924faf04b
Author: car <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 705202e2e4d1f3cea532f9cc08632f400e718112
Author: car <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 d363e19e6e6668c55937ac5829b5485acdce3f6d
Author: car <car>
Date:   Wed Aug 19 17:22:00 1998 +0000

    Minor changes.

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit ee526c123e5427ca7c24792e137000008f0314ea
Author: car <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 023511f96d7603fa699be254cc6bef5e347d36fe
Author: car <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 df7a663a1f3e7b2e55627f4c0a43c20867469d23
Author: car <car>
Date:   Fri Aug 14 16:37:34 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit 174066e21cd0f617b0d18ffe31cb881452a58b82
Author: car <car>
Date:   Fri Aug 14 16:36:19 1998 +0000

    Fixes for WIN32

Src/C_BaseLib/FArrayBox.H
Src/C_BaseLib/FArrayBox.cpp

commit 251295b9ce2a2337d5dcb7f5753225f80ef382d2
Author: car <car>
Date:   Fri Aug 14 16:28:19 1998 +0000

    added portable support for quiet_NaN

Src/C_BaseLib/FArrayBox.cpp

commit 2a8afd48e81171ea2cfefe2999946256f549d444
Author: car <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 3ca0cbe5afbc1969cc407554743cc943cab1a1c6
Author: car <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 57e67dfc5d41719debbfa3a5de900028a612854f
Author: car <car>
Date:   Thu Aug 13 22:54:40 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 78d09767d022606b4a60e2124c1be14736aba265
Author: car <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 06a6729f1cbf94655818eee0adca6b7baab576e0
Author: lijewski <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 f15f4d21f8e5de4610a84deeca6e0e04d7d8ce66
Author: lijewski <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 794c4ec7b68a14699302138e4e369f5f24c300c6
Author: lijewski <lijewski>
Date:   Tue Aug 11 20:33:20 1998 +0000

    Added mpi RunStats.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 8e605cebccf49ba1a0c4c3cde3e362684bd187ae
Author: lijewski <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 787b7b6560c790c475e77b51bcdd2491e2e1cba4
Author: lijewski <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 9fe2a51522b53693d387edcfb62fff45d8df42aa
Author: car <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 e45483ef193af3d0c5f14de7525236f0964ddeaa
Author: car <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 10208691aa2058cb1ce050e5704f762177552677
Author: car <car>
Date:   Thu Aug 6 20:56:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit 5abff0168516d716a637cd24c40c141723a5457e
Author: car <car>
Date:   Thu Aug 6 20:31:09 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit d3388ac98b339c73ceb568f07412a5db1d0e86ca
Author: car <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 7d4253e6c6eb258e4ffb46bb5ea1fd32d28cae81
Author: car <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 08bc7c2665412566fc185ad36c5ac783ac50927d
Author: car <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 fbb95001f0b6191b17ae8e4b78567b98d6e5dd89
Author: car <car>
Date:   Wed Aug 5 21:24:42 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 5fa7d7b60bbb7c88c6191ba2b1c50715922a783d
Author: car <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 007cfb6e9849c5e05da601f500aaea84edfe7373
Author: car <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 f8d3229288dbc5dce9daaefb33d10876e896e76d
Author: car <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 e115dda27f62ee113bb17fbbe5a0d85cefd10160
Author: car <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 c125fa3ab24760bc37c51ed60b1d56c0fa288d44
Author: car <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 79dd7a9adc41dbbba69612d75040c24edecb50d9
Author: car <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 d1c3a2bc4a6b9ffd48ab63d441a0c054c76111f2
Author: car <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 e13e57670382dbca52f93356f6f2e33a0c83b4cb
Author: lijewski <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 bb3ec38dfd561cc40ae83cd7f07856b2333e1f16
Author: car <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 b7a7ff9995f8b7701dcbb45d18901aebe2a88645
Author: car <car>
Date:   Mon Aug 3 20:02:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.cpp

commit 9b327ebfd51915b6b698fe569c1f8b2aa6c1d5ab
Author: car <car>
Date:   Mon Aug 3 19:26:26 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ebbcc980f3b957c7724b1e1d77951b76caffd80d
Author: car <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 679f6914e0ac47151744c6bd3761cb999ffb8184
Author: car <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 b0815ad94beb95de0cf13e4729629bfca08b840d
Author: car <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 6d94a74e21b57539482876ebf434e50658bb5c39
Author: car <car>
Date:   Thu Jul 30 23:13:45 1998 +0000

    more preload removal mods

Tools/C_util/README

commit b2098def6a6026dc2590862aafc00c1e87a44b24
Author: car <car>
Date:   Thu Jul 30 23:06:43 1998 +0000

    Rid ourselves of BSP files...

Tools/C_util/preload.cpp

commit 15db0bbaa5f0448f68038e7e30a1c1715f92e0bf
Author: car <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 89e694a20d0ed460e009d8321602232905b87ed1
Author: lijewski <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 15dd75d476de16e43c36ff87b254834e45016bf7
Author: lijewski <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 b7e2bbc06e0526d6a36897213c8e46a5920765ce
Author: lijewski <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 485500429a2cd95e69a7f53778fe5cc97ac81605
Author: lijewski <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 9030d8571f83858bd1adfe7c5f7b7eef642c11ee
Author: lijewski <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 3b1547bdaf4c8869499a7369c74d312a95b519fd
Author: lijewski <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 96b9b8da958f5a3afb204b48d3e7b43f0987a4bb
Author: car <car>
Date:   Wed Jul 29 17:21:30 1998 +0000

    Added comment for Windows.

Src/C_BaseLib/Utility.H

commit d5b0688f85d231c49f7493d735a18590c24f4149
Author: car <car>
Date:   Wed Jul 29 00:06:04 1998 +0000

    Dosify.

Src/C_BaseLib/Utility.cpp

commit 03ab66c88ff98fc63527503489dc985c980e7990
Author: lijewski <lijewski>
Date:   Tue Jul 28 17:47:49 1998 +0000

    Undid the static RunStat -- T3E had a bug.

Src/C_BaseLib/DistributionMapping.cpp

commit 983a7ea49f2ebc9dcac7d88b0245c3ab46f852b9
Author: car <car>
Date:   Tue Jul 28 17:16:06 1998 +0000

    Added ccse-mpi.H as a T_source.

Src/C_BaseLib/Make.package

commit b9b41c38318f0c73abae5183e3d248488ecfb078
Author: car <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 f7d6ecedae89a0c4c65d3d5891a9628a6293cddd
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:33:36 1998 +0000

    Now using <ccse-mpi.H> instead of <mpi.h>

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit 1c6ee150c88ce41e7c6ea8aab39122d84e60f1fa
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:33:06 1998 +0000

    Now using <ccse-mpi.H>

Src/C_BaseLib/FabArray.H
Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/VisMF.cpp

commit 9035c2abfdaf9d10ffe56145d59e0be31c6dd161
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:32:46 1998 +0000

    Encapsulates <mpi.h> making it slightly easier to change from
    using BL_USE_MPI or not.

Src/C_BaseLib/ccse-mpi.H

commit 4fcd9ade357920b0ab2c60c2e1c0e2bc92de7d91
Author: lijewski <lijewski>
Date:   Mon Jul 27 21:14:16 1998 +0000

    Made RunStats(fabarray_copy) a static object.

Src/C_BaseLib/FabArray.H

commit 33794cdd02d605804142e5717e9dd5252ccf48ea
Author: lijewski <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 41c9b90fb7ea8fccc9725a5666be1fb13aeef1f9
Author: lijewski <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 f95be54806f75136e8d886acad73bae55cfd7fa0
Author: lijewski <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 162f8b6ae051c8b6b4fede08f2d9e18e840156f7
Author: lijewski <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 765c667f4c6c8fc6aeeb4ba94bb7747f257efe98
Author: lijewski <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 6fe17cac9f432094caa616856714ffbcdf6fff13
Author: car <car>
Date:   Thu Jul 23 16:34:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 794045ce5858735a3fbcf44d0b55aa9279af8332
Author: car <car>
Date:   Thu Jul 23 02:49:27 1998 +0000

    Not needed

Src/LinearSolvers/C_NodalMG/Notes.doc

commit 6f9863c1118b358861a5e5097ee2ed5e5ccd7dc1
Author: car <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 57c624c594de17c6b4c328ca8afacc21f1a37d57
Author: car <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 3605dd2ebe46f3838819e30f56b0008981b67c64
Author: car <car>
Date:   Tue Jul 21 17:44:45 1998 +0000

    MSVC change

Src/C_AMRLib/TagBox.cpp

commit ce3c2836480db709d06c3f3fff6987a9511aedbe
Author: lijewski <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 2f470ac120279c0a8e363bc8e84d7db1d9b854c9
Author: car <car>
Date:   Fri Jul 17 17:59:07 1998 +0000

    Testing.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 2cb093275c08d8a72a3d7f4960a96edd12fb0c85
Author: car <car>
Date:   Fri Jul 17 17:32:59 1998 +0000

    Minor changes.

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit 82d3ee109d905d79cff863a1d8ed2663ada40dba
Author: lijewski <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 3b9549d8754c04a0360b0ea095a5f20dd076ed03
Author: car <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 2172b1188966f260a12c63a54afbaa11739507cb
Author: lijewski <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 03da4ee53fb957d688eba4aaa60ac9ae28d241f7
Author: car <car>
Date:   Tue Jul 14 20:47:26 1998 +0000

    test

Src/LinearSolvers/C_NodalMG/Notes.doc

commit e838de8b51745f07687efe71c75688822b8e6bc0
Author: car <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 6a90849e2c05c1296c1ee84a63b4c187a312b197
Author: car <car>
Date:   Mon Jul 13 21:40:42 1998 +0000

    First CHeckin

Src/LinearSolvers/C_NodalMG/Notes.doc

commit b33116cde52aaa784a503928a6ccfd11da642534
Author: car <car>
Date:   Mon Jul 13 18:17:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit e6b61468f222a9752446318d558e2e0dc0b00c94
Author: car <car>
Date:   Fri Jul 10 22:32:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgparallel.h

commit e935e1d652ba1fe6e8e734001abe988b0ffe227f
Author: car <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 bd91e2f71567ccad5ddf2304b3e09ea73361643e
Author: car <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 f5abc83f76dff2d19ba47f1141ba4c04008de3a6
Author: lijewski <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 e569238abbbf0bc0c8a1de470c967be49e650b4f
Author: lijewski <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 b07338ec1e04f88955fe54c1779d09789fd3f5de
Author: car <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 955335d8250861659872020751f63d31f02f5da3
Author: car <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 8fbd155950a8880e9e6f871dc05b744f6ac61d8d
Author: lijewski <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 02f7e3f533cbd09857f0208ed6f069c08ec902be
Author: lijewski <lijewski>
Date:   Wed Jul 8 21:56:21 1998 +0000

    Fixed very subtle bug in FillBoundary() caching mechanism.

Src/C_BaseLib/MultiFab.cpp

commit 3f3fa8d46f29085d2df28140a417ebb9889c602b
Author: car <car>
Date:   Wed Jul 8 20:19:57 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit a8ee404a15d2cf41b3798314a1d6b50af5f54810
Author: car <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 af1c9464de0f3298074d39e107e50270f975ac0d
Author: lijewski <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 7a71136316a8c1b4b5c0023d5ca1aea36756cad3
Author: lijewski <lijewski>
Date:   Wed Jul 8 19:17:16 1998 +0000

    Added MultiFab::FlushSICache() in appropriate place.

Src/C_AMRLib/Amr.cpp

commit fe137c9680605f7e1cfc925c7ee863c2566213c6
Author: lijewski <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 eb8c317e5df94b13ffbb5a79b7ff248199909f13
Author: lijewski <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 be781b513914c6f8b8b7b66a2865afd56ca63eff
Author: lijewski <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 e63bcae781efb6dcfbfb48fe311cd40406a55ffd
Author: car <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 f8632161602bb53a33016e361d4be5498322fa05
Author: lijewski <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 467e67b3505225ea510f1e898b8d1bc34f8df8f7
Author: lijewski <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 deb7c3f1f869191cc7de37e1213b01de7c77d08a
Author: lijewski <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 3ea83e5fac5aad9aab7013b866bb766939c513f6
Author: car <car>
Date:   Tue Jul 7 15:41:52 1998 +0000

    Support for g++ 2.8.1

Tools/C_mk/Make.defs

commit 754652b595de30289816fa70b1dab04634fe64fa
Author: lijewski <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 c57eddb2f93289fc1b871db3769f1e410ae6fd0b
Author: lijewski <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 4840c7b81fa724b9a64486c1fa4285c9d22d9f0d
Author: lijewski <lijewski>
Date:   Mon Jul 6 20:44:18 1998 +0000

    Now use pubsetbuf() instead of setbuf() by default.

Src/C_BaseLib/VisMF.cpp

commit e2be62ecc3b37c7b479ccd8d934da5df66ec49c6
Author: lijewski <lijewski>
Date:   Mon Jul 6 20:44:00 1998 +0000

    Now use pubsetbuf() by default.

Src/C_AMRLib/Amr.cpp

commit f3993df69ae507281ca8aec608d096107b2d0a57
Author: lijewski <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 ac7f3aa07d83fe87c1ed6cb81f2b945487ac1243
Author: lijewski <lijewski>
Date:   Sat Jul 4 03:35:14 1998 +0000

    Fixed bug in FillCoarsePatch().

Src/C_AMRLib/AmrLevel.cpp

commit e1e04edb5c2bb679643903978bdd6c23d82a7ffc
Author: car <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 ab5273f2bbaff483b3b64429a13ecc1d1c55b4c8
Author: vince <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 c69cc6b6dd724f1657d7d70a32e72346e7e85603
Author: lijewski <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 cdb659e5c140792f73744b4ae1990db9dacf15d5
Author: lijewski <lijewski>
Date:   Tue Jun 30 23:43:45 1998 +0000

    More simplification to FillPatchIterator.

Src/C_AMRLib/AmrLevel.cpp

commit 23dd6aa740dfc451b5d19333038519b2f336cc70
Author: lijewski <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 8f0a2bac6616a64b011d9d90531798374eb91f6d
Author: lijewski <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 81865f1e5014e662a20cf3c448645d5e31b9087e
Author: lijewski <lijewski>
Date:   Tue Jun 30 04:08:16 1998 +0000

    A tad bit of cleanup.  More needed.

Src/C_AMRLib/Interpolater.cpp

commit 932450e3b9a37a1cc5e1f6c256ecdef1430a626d
Author: car <car>
Date:   Mon Jun 29 17:03:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 172595fffcd810bb189767bf332239a698e28943
Author: car <car>
Date:   Mon Jun 29 17:01:54 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit ccefddec778b88dd61d1af52d264f6aa0d9b62cb
Author: car <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 22c89a74fa2ccc99704fc6c46a4814edf8c9a85d
Author: car <car>
Date:   Mon Jun 29 16:34:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 8588295485449eb7fe8e827898d4aa0a653d3cd4
Author: lijewski <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 bfaf56a3b1d62a9171f517cc097353634e18548e
Author: car <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 dbc844c5e13d8fae00c60f77f63f76ee96787434
Author: car <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 415e30d1ae8587e56353de1b47bd688acc14f357
Author: car <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 16e41cb8936a255f94ba5548a3d567d38207a98e
Author: car <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 f1981df61c70fd9715c4581a97db6732fbb6dc80
Author: car <car>
Date:   Thu Jun 25 16:34:37 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 9e458484ce54f6860827013ef1c559a746b4a439
Author: car <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 d35510814f7ae67d619701650a0965dfb9e9db8e
Author: car <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 411c96aca5dc622df51bca351ebedd9504e8e9aa
Author: car <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 9a5083fa8874e1599531449374bb20d31f2b678c
Author: car <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 10cf77a7e7d8e79b5047ce059ce9523a749fdf84
Author: car <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 13e8f84cf9b6fd53e0261af7f7085d80cc4c8037
Author: car <car>
Date:   Wed Jun 24 17:26:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 7f064dbc747e63f66ff03ea74a43111484704b2c
Author: car <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 d08288b885ba317206f2431eda6b4a507d396076
Author: car <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 6eeb04d508fc40d9684dff415fc6fc790ce9852b
Author: car <car>
Date:   Sun Jun 21 22:10:35 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit 69be6883dd8c39175842910aa39c5867bdb18084
Author: car <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 c66ece1948676785108625dea0b752360321d157
Author: lijewski <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 c229d9c30402b7a0df164d271610dd6027430fab
Author: lijewski <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 33e89c8fe55c2f3904e519674396879bfa3c2e73
Author: lijewski <lijewski>
Date:   Sat Jun 20 16:16:09 1998 +0000

    Added copyright notice macro.

Src/C_AMRLib/Interpolater.H

commit 633a460d95812c6a74818a52b0194d46a8ac7f6b
Author: lijewski <lijewski>
Date:   Sat Jun 20 03:20:02 1998 +0000

    Fixed bug in mapPeriodic().

Src/C_AMRLib/TagBox.cpp

commit efed1cc469397715266be52febaaa47d10e28298
Author: car <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 f3955f2b7a210de23fa6ca5501e5182b98f94c01
Author: car <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 bdc7f5dae242534a53fb50a724ba2a6c92b25e6f
Author: car <car>
Date:   Fri Jun 19 18:18:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 4bf971d51746922cc2be0ad92ea186e076aba81e
Author: car <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 f889f5d7e31c53fe044ef330867fedf608a7a9a2
Author: lijewski <lijewski>
Date:   Thu Jun 18 23:45:52 1998 +0000

    Added another assert().

Src/C_BoundaryLib/FabSet.cpp

commit 8005805006ecbcd15a8ae7fec0fb682f8e46fc1f
Author: car <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 71eeaa3e0a792707ffc9c123164d36f96c82b010
Author: car <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 1cf82a23ecaccb03b5df29f617932ea97682251f
Author: car <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 c144a79a6279c685e4d4ba1401259113560d9e1d
Author: car <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 bd14e91d873b2927586cbec69cb29d353ee6add9
Author: lijewski <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 4b859a41aacfa2e453ad8f272381c4f329295300
Author: car <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 67e915b53391f7f10c0209f32f3fc91d21814ea1
Author: car <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 c2cf6e594a54b930313777e9e2e3a846a960f9e6
Author: car <car>
Date:   Wed Jun 17 18:16:57 1998 +0000

    2D Changes.2D Changes.

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 463a91959d376534fce6a6ff37161f7739034c91
Author: car <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 7a62ed5399b7fc51b377e2eed2390047f72865e7
Author: car <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 e75c09420c3d8d1773053a02414cfef9a61a5454
Author: car <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 8d47ca3625fc533cb62d03a1c04df7d06bef89d3
Author: car <car>
Date:   Tue Jun 16 23:30:05 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit cdf50693ac914da1496404b3245b7d22d3c76950
Author: car <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 9d9f353d2f211dc0e74d8717b42886dd5db6580c
Author: lijewski <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 0b8283371464b3b023e12cd9a3bc636940583e71
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:01:37 1998 +0000

    Removed call to FlushSICache().

Src/C_AMRLib/Amr.cpp

commit eee472c2de77c73d72eaf47c15bcefec80909a0f
Author: lijewski <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 fcf7e67b8a08e6227c968711d68789aa365992d7
Author: lijewski <lijewski>
Date:   Tue Jun 16 18:00:46 1998 +0000

    Made FabArrayCopyDescriptor::clear() really work.

Src/C_BaseLib/FabArray.H

commit 34490600ebd8622fb2dd61a33b9f65b89c37b34f
Author: car <car>
Date:   Tue Jun 16 16:02:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit c05d5ba365e6efa6ae3657db501620fbdef7d9c2
Author: car <car>
Date:   Tue Jun 16 16:01:06 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit ea6e6271240198016287e99933aea1a8e96364d9
Author: car <car>
Date:   Tue Jun 16 15:59:43 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 7742841d0d357066184e5cd40054c7e802af863b
Author: car <car>
Date:   Tue Jun 16 15:41:38 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit a908a29917e1d4d7f490f4d6e7cc696333b9853d
Author: car <car>
Date:   Tue Jun 16 03:39:03 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit 01b01a3aa32a01b5c5dafeb41d21f5b775e858ea
Author: car <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 4a84e4d6cc701e737441be9fb383012137b62d4d
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:55:36 1998 +0000

    Added MultiGrid::FlushSICache().

Src/C_AMRLib/Amr.cpp

commit 6fb6ea6a2c96af797ccd30ec7595bee5ecf07a50
Author: lijewski <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 c6a0ed164acd968030eb14db750fd18b94e7165a
Author: lijewski <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 e45ca94d4f9e68a25da6a47b0445c1d994f11c45
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:53:44 1998 +0000

    Inlined operator==()s.

Src/C_BaseLib/BoxArray.H
Src/C_BaseLib/BoxArray.cpp

commit 163788f5968a2952684dedd7debd4cdce2f8811d
Author: lijewski <lijewski>
Date:   Mon Jun 15 23:52:57 1998 +0000

    Simplified operator==() a tad.

Src/C_BaseLib/Array.H

commit 65d766483954b56d98fd9579a4893cd233db1a49
Author: car <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 3d4ec5cb5927a196d925c4356e44be8579364707
Author: lijewski <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 57ce3103b2b9580058aa91b73b2385b928b5645b
Author: car <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 3e5773e32432cdf123390035ba7841c26028aec8
Author: lijewski <lijewski>
Date:   Mon Jun 15 15:13:25 1998 +0000

    Added fabarray_copy RunStat.

Src/C_BaseLib/FabArray.H

commit 8b3b3bf6af182eb9c92a54cde938d342305c5fcc
Author: lijewski <lijewski>
Date:   Sun Jun 14 22:05:38 1998 +0000

    Removed default size initializer on cache.

Src/C_BaseLib/Geometry.cpp

commit bf46ef40f97c5e0a97a8a045c42c9cfea7c0aa69
Author: lijewski <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 38d36a14eb8dd161b7d5baddd72742794eec93a5
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:12:28 1998 +0000

    Added more RunStats.

Src/C_BoundaryLib/FabSet.cpp

commit 060c83eda88e567d5f8231ee42c1692b08c3a162
Author: lijewski <lijewski>
Date:   Sat Jun 13 21:07:34 1998 +0000

    Added reflux RunStat.

Src/C_AMRLib/FluxRegister.cpp

commit 96f54fc316fa9a64727c486b84b230e3b0b11970
Author: lijewski <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 45cfc77319d7eb4b31fe8c132364332de90ae0c5
Author: lijewski <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 268aa7d4068988d171587a1edf6c88fa37248ade
Author: lijewski <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 5ceb440691ee08060545f3d222d29341cd0cd5e8
Author: lijewski <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 6a929bf1a8cd8517ff78f31d5538fad088b36dc3
Author: lijewski <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 31f369285847bd84741c0f3f44a60823c5806a85
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:49:43 1998 +0000

    Added a CacheSize() member.

Src/C_BaseLib/DistributionMapping.H

commit 5a54165d5efff962532b19bf540df9509eb435c6
Author: lijewski <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 08f292a438ee7e35c23ab06f901d4ec29aec054c
Author: lijewski <lijewski>
Date:   Sat Jun 13 15:48:11 1998 +0000

    Now flush PIRM cache at appropriate time.

Src/C_AMRLib/Amr.cpp

commit 4b102fc3cc30e431802cde100f6a64d265fb4c29
Author: lijewski <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 36543d75b5667480a9ce9c033d92187ac5f9d79a
Author: lijewski <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 b591d0b6482e28bb037fe365e15c622adc525112
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:47:08 1998 +0000

    Added BL_COALESCE_FABS.

Tools/C_mk/Make.T3E

commit 8d1ad158a7b0e28ec80ab37cc6d0e7f9b79b7a2c
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:37:57 1998 +0000

    Unary + and - operators are now const.

Src/C_BaseLib/IntVect.H

commit b6ae265d4fc35ae6e7209ccb4d98aa4acf728f61
Author: lijewski <lijewski>
Date:   Fri Jun 12 16:25:18 1998 +0000

    Performance mods for second Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit e66d5561e4e0f540ae18216ae97a122e27c167e0
Author: lijewski <lijewski>
Date:   Fri Jun 12 00:11:14 1998 +0000

    Performance enhancement to first Reflux().

Src/C_AMRLib/FluxRegister.cpp

commit 10f17f08af0962957bf203de7276618fef694137
Author: lijewski <lijewski>
Date:   Thu Jun 11 22:37:45 1998 +0000

    Performance mods for mapPeriodic().

Src/C_AMRLib/TagBox.cpp

commit 27001f90d0d60bdae05c8b201d0514e8ff5386e5
Author: lijewski <lijewski>
Date:   Thu Jun 11 21:24:25 1998 +0000

    Performance enhancement to CrseInit().

Src/C_AMRLib/FluxRegister.cpp

commit 1bb988c51bfe279695802d24303804fdbe2923a7
Author: lijewski <lijewski>
Date:   Thu Jun 11 18:21:29 1998 +0000

    Some FillBoundary() optimizations (hacks?).

Src/C_BaseLib/FabArray.H

commit 117a1ecfecb1b93a175454b80265ddc38f893e84
Author: lijewski <lijewski>
Date:   Thu Jun 11 17:23:10 1998 +0000

    Some performance enhancements to copyFrom() and plusFrom().

Src/C_BoundaryLib/FabSet.cpp

commit b7e0e497e676c1653acf9c3ee4d1a357c9b34fe1
Author: lijewski <lijewski>
Date:   Thu Jun 11 00:06:16 1998 +0000

    Fixed little bug I just introduced.

Src/LinearSolvers/C_CellMG/LinOp.cpp

commit 773b1a48001ccaa981489c809ec462eb4f28c1fb
Author: car <car>
Date:   Wed Jun 10 23:30:13 1998 +0000

    windows fix

Src/C_BaseLib/FabArray.H

commit 64e926f1f4db4e2d2b4f86e32c8a987cbd92374c
Author: lijewski <lijewski>
Date:   Wed Jun 10 22:24:32 1998 +0000

    Added RunStats to FillBoundary.

Src/C_BaseLib/FabArray.H

commit c7f2bcb85d50e5e1bb4d09caaf8a7d681ec33c38
Author: lijewski <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 a50e7e4e9722df5e6930d81e25040ed9b2779cae
Author: lijewski <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 dfc91906f8ae0fae9ae47b9409a8458cda3c7ffd
Author: lijewski <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 2dca999ec4eebd18a4b60827d35a8511381321d7
Author: lijewski <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 a134bff23972343a0cf81b149cc6350fb6e6ff0f
Author: lijewski <lijewski>
Date:   Wed Jun 10 18:23:01 1998 +0000

    Added test for periodicity in FillPeriodicFabArray().

Src/C_BaseLib/Geometry.cpp

commit 3f19b0ac3553f3e43340f1dd6e84e4723101db2a
Author: car <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 8a8943e450f5b9535f33b27b782aef26f2080d14
Author: car <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 5602e4e30d15de01f0b95590202c1099a9907c3f
Author: lijewski <lijewski>
Date:   Tue Jun 9 23:04:48 1998 +0000

    Added fill_patch RunStats variable.

Src/C_AMRLib/AmrLevel.cpp

commit e7051171a985c9f35700da66111e2144d523b517
Author: lijewski <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 cd3a323fbe7a060eb6c5e5ec4600db9f81937bcc
Author: lijewski <lijewski>
Date:   Tue Jun 9 15:02:43 1998 +0000

    Enable BL_USE_SETBUF for OSF1.

Tools/C_mk/Make.OSF1

commit fa5843a6b6036358464c7e3867150ecfc5ea73ef
Author: lijewski <lijewski>
Date:   Thu Jun 4 17:12:38 1998 +0000

    Dealt with multifab copies taking nghost.

Src/LinearSolvers/C_CellMG/CGSolver.cpp

commit dafd1ba7412f44d0aa22daefd68da8aa795f1c43
Author: lijewski <lijewski>
Date:   Thu Jun 4 00:16:32 1998 +0000

    MF-MF copy never mucks with ghost cells.

Src/C_BaseLib/FabArray.H

commit dbc114648b5093d6d67107cef278430703683dc3
Author: lijewski <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 494a2a7ec8b6da76894c43ae5b8d31fc8a1d81b2
Author: lijewski <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 2c5466e89c624270939a88ef2be08ebc3ce3e0d8
Author: lijewski <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 6fdc1fc25538fd0a2e5e21a6f67438320efda7a3
Author: lijewski <lijewski>
Date:   Fri May 29 19:46:52 1998 +0000

    Removed a couple unnecessary lines.

Src/C_AMRLib/TagBox.cpp

commit 82bb64a255d90863ffa63814b5c9aa8941e3b357
Author: lijewski <lijewski>
Date:   Fri May 29 18:01:37 1998 +0000

    Added toDouble(), toInteger() and toLong().

Src/C_BaseLib/aString.H

commit 8621f57ed33a13d1f1784e7eff7c5da925f3839c
Author: lijewski <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 3e43b6cc7ad43d4dbddfe9ba28595df9636ba8f7
Author: lijewski <lijewski>
Date:   Thu May 28 21:34:01 1998 +0000

    A little cleanup.

Src/C_BaseLib/MultiFab.cpp

commit 0e37e973b4464691d4c30c95edbc5ce6200670e9
Author: lijewski <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 1eb0857e05dd72d99c6b196f03de23de7308e65d
Author: lijewski <lijewski>
Date:   Thu May 28 21:32:03 1998 +0000

    Some more cleanup.

Src/C_AMRLib/FluxRegister.cpp
Src/C_AMRLib/TagBox.cpp

commit f0508c21ccab87492f454c80c3a32fdc39768cea
Author: lijewski <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 e34584cd349f6831a972a514f8cf7331221fe469
Author: lijewski <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 4d4893bfc79a6ba01b1665c534538fb30506dec4
Author: lijewski <lijewski>
Date:   Thu May 28 02:50:44 1998 +0000

    Using different FabArray::copy() in copyTo().

Src/C_BoundaryLib/FabSet.H

commit 0382f4f1f5a455b4e6b726bdc7f06dfac6490cfb
Author: lijewski <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 0a3568f071876f5cc63ea1e9c625949db570de8b
Author: vince <vince>
Date:   Wed May 27 22:46:11 1998 +0000

    Added Broadcast for MPI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 22bb2ce03152b7e75db8d6e1673770d44c6c60f9
Author: lijewski <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 1a896efc7b5cb406aef5f1468fa70b66565b1651
Author: lijewski <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 367acbaee06e3c8567eaf0348e41fc5d86505a5f
Author: lijewski <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 539345f912154875620e8c0692fca0c54d124142
Author: lijewski <lijewski>
Date:   Tue May 26 17:08:54 1998 +0000

    Integrated in vector<FillBoxId>::iterator.

Src/C_AMRLib/FluxRegister.cpp

commit 3bb35c72513baaf54e1436dedcd41f6bf566d4cc
Author: lijewski <lijewski>
Date:   Tue May 26 16:17:16 1998 +0000

    Oops.  Didn't check BSP.

Src/C_BaseLib/FabArray.H

commit aa21e359e0d43b46db42069e05041eedb82eb591
Author: lijewski <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 463c99a3a6cdbc921b8d041e48a38e8961b6b8ba
Author: lijewski <lijewski>
Date:   Tue May 26 00:01:48 1998 +0000

    Optimized size of temp FAB used in CrseInit().

Src/C_AMRLib/FluxRegister.cpp

commit 4775cdb3ade185292ab9e5b4c88f6825dfca177c
Author: lijewski <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 d3299d7c2703e2ccad62726ded19c5ab8eaf3940
Author: lijewski <lijewski>
Date:   Mon May 25 06:01:24 1998 +0000

    Fixed bug in FillBoundary().

Src/C_BaseLib/FabArray.H

commit 868f65d7e04b8cc5e1db5826c94420d055fcd232
Author: lijewski <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 ba558424cab579716bb9366485f9475761de1146
Author: lijewski <lijewski>
Date:   Mon May 25 05:01:10 1998 +0000

    Minor fixup.

Src/C_AMRLib/TagBox.cpp

commit e8eb1ff7952a70522565a2e6864a3ac48afbf3e2
Author: lijewski <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 d13fc15f84bcd3ec66aa5f32b034bad7f7c0d711
Author: lijewski <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 5f7c2e4659bf80ddd6ecb282fd3cf88b53d77213
Author: lijewski <lijewski>
Date:   Fri May 22 23:31:31 1998 +0000

    Only communicate overlap in copyFrom() and linComb().

Src/C_BoundaryLib/FabSet.cpp

commit 4a12514831a84f2c922fb3aef9d42fa8fa07924c
Author: lijewski <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 75b73cf9f232643a648a5eb42a290dc7e37c9bc7
Author: lijewski <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 cb3e41467db8c5d6b5436359a3cdf9b8cb5e5120
Author: lijewski <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 21e5b6b36a9fe47bb158410ad0561059783a1829
Author: lijewski <lijewski>
Date:   Fri May 22 21:52:49 1998 +0000

    Added copyTo(MultiFab).

Src/C_BoundaryLib/FabSet.H
Src/C_BoundaryLib/FabSet.cpp

commit ab97d22ae192dc87d15d9532c821ae8fa159e8cd
Author: lijewski <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 5a6d83f12ecc6ee0573921cf80fead5b41a0e13f
Author: lijewski <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 0a3fd5a50eba7b5526001888c35ccbb623a4f1d9
Author: lijewski <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 1707d92cd781a14aae01b27e6c996e85daaac40e
Author: lijewski <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 bf3455328b4203b10dff13278a908abc49c7eff9
Author: lijewski <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 424bc4fac80c67492608b65c15a6c3f4cb1a05f3
Author: lijewski <lijewski>
Date:   Thu May 21 22:44:51 1998 +0000

    CXXOPTF=+K2

Tools/C_mk/Make.T3E

commit eb3dad0708a4a4c04c5bc134b472b4adcf9fe0cc
Author: car <car>
Date:   Thu May 21 21:28:43 1998 +0000

    assert foolishness

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit a28d2bc7c5eda3dfa47905e7c11cea30efa0209a
Author: lijewski <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 892f18b47b39782f7c3a388aa4b56133f230b125
Author: lijewski <lijewski>
Date:   Thu May 21 16:48:39 1998 +0000

    DependentFabArrayIterators now check for equality of processor maps.

Src/C_BaseLib/FabArray.H

commit ab7ffc5cc06a3d8d463f1a367ac5a07b1f189866
Author: lijewski <lijewski>
Date:   Thu May 21 15:04:29 1998 +0000

    Removed DependentMultiFabIterator stuff from FillBoundary().

Src/C_AMRLib/StateData.cpp

commit d42f519ad18667b6809aacaaf500ac461f79e93f
Author: car <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 1fdab4261eda62fd3971ec2dfad2ee05280b89f6
Author: marc <marc>
Date:   Wed May 20 00:10:45 1998 +0000

    Make contains() const

Src/C_BaseLib/RealBox.H
Src/C_BaseLib/RealBox.cpp

commit 6d4f14a3e5695db7225091fe36790cf46d79d9b2
Author: marc <marc>
Date:   Tue May 19 21:08:35 1998 +0000

    Fix a couple of little errors.

Src/C_BaseLib/Geometry.cpp

commit 98eefe6ec55351fa4031cf48c4863862f6fcc919
Author: lijewski <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 8a24a890ab11643972a7456c265763f0dac50a77
Author: lijewski <lijewski>
Date:   Tue May 19 17:10:52 1998 +0000

    Moved allocation of pshifts outside of all loops.

Src/C_BaseLib/Geometry.cpp

commit b23c99855d33c5df8e968baad69e2c0b835a977d
Author: lijewski <lijewski>
Date:   Mon May 18 17:52:20 1998 +0000

    Some cleanup/simplification ...

Src/C_AMRLib/AmrLevel.cpp
Src/C_AMRLib/FluxRegister.cpp

commit 1a15e88c3eb05cd609023dbf37968d18445cdf40
Author: car <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 78cdda8f717e07bf934b15fd680318d449aba889
Author: lijewski <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 e325078439ce20f0f37d54cd6c6cad81154e5fee
Author: car <car>
Date:   Fri May 15 22:31:29 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit feb564285830642f75497aa77ca536ae809b4801
Author: car <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 a488695861c248581cbbaa0f4a654bbf5d8fed8f
Author: lijewski <lijewski>
Date:   Fri May 15 18:13:12 1998 +0000

    Fixed bugs in TagBoxArray::mapPeriodic() and TagBoxArray::coarsen().

Src/C_AMRLib/TagBox.cpp

commit 2752cdb382deb3c1c06fce9e7fdd0dad0a33ede8
Author: car <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 2f17a886cd9b761563ebc0cda5f669858cfa51ef
Author: car <car>
Date:   Fri May 15 16:16:22 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit a10bce6b33a83bf105edef470034e8d502bb8edb
Author: car <car>
Date:   Fri May 15 16:05:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 8ac19652c9550ad8f80e002f2173497a6d298e89
Author: car <car>
Date:   Fri May 15 00:32:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit b1d3ad8c402f324b4443165eff3eddcbe3e5dd14
Author: car <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 196f33518fa19219cb852828f86df2ef60fbb982
Author: vince <vince>
Date:   Thu May 14 22:23:04 1998 +0000

    Fixed minor bug due to TagBox changes.

Src/C_AMRLib/DatasetClient.cpp

commit 31cfeb4d80d42ebe4251b7ed27403c01f0266bd0
Author: almgren <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 13c4779f8046c67aa784d8792be58043cb78aff5
Author: lijewski <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 f928078d6705184bb26c28b3da8a9d0e5e293adc
Author: almgren <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 c1f570493fd817b331b72e518315ce57c133025f
Author: almgren <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 b81b0f05a6c2fb23464b0fe8b38d52ae6ea40eff
Author: lijewski <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 bab2c671459c15272ee5c584adbc3d9b35bf1710
Author: car <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 4cbf49e26c23136e1a540dc1b552c0fad07a5ab1
Author: car <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 2abbe2ad3ea020e245f273f018c252462c6e8219
Author: lijewski <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 b3b635e0cf7b18a3405e4d21dcd4fd5620295731
Author: lijewski <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 628f413da6ba988e5457d25a0340ed4784d2a65e
Author: car <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 6a7f584d675250843b2b3373df46f297ae4c08ec
Author: car <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 5367e2ff05ca919f8bf28ab6f77f064b9e0e9268
Author: lijewski <lijewski>
Date:   Fri May 8 15:58:50 1998 +0000

    Added more Doc++ comments.

Src/C_AMRLib/FluxRegister.H

commit 9b1f50a42174838fe6733881ea567864c817d0f1
Author: lijewski <lijewski>
Date:   Fri May 8 15:57:12 1998 +0000

    Updated Doc++ comments.

Src/C_BaseLib/Box.H

commit 50116d837fba3e7caa7641e606ad19f55c3a21c2
Author: marc <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 74f6da13dfb38a3d8926038a1cde95d465c63564
Author: lijewski <lijewski>
Date:   Thu May 7 22:26:09 1998 +0000

    Added ResetWallClockTime().

Src/C_BaseLib/Utility.H
Src/C_BaseLib/Utility.cpp

commit 2835d63c33db7cd0d068ebd06e4913e5db8348bd
Author: car <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 85df81bf20fad64d1ca3862a1ffeeef1ba5d63b2
Author: car <car>
Date:   Thu May 7 18:28:59 1998 +0000

    Microsoft VC++ bug with nested classes

Src/C_BaseLib/Geometry.H

commit 7c299d637344479a114d6762e0e18f568c936478
Author: lijewski <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 04f6e3a2f05e6deda8f6cbb5e86aa286813d25b8
Author: car <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 29a476612c11eb7d4b25b7ab9c88cfe90f09e9a2
Author: car <car>
Date:   Wed May 6 20:11:54 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/fill_patch.cpp

commit a76fe3014c9100bac09f27eadd48ab5c95ed14a4
Author: lijewski <lijewski>
Date:   Wed May 6 17:52:43 1998 +0000

    Gunk for doing doc++

Src/C_BoundaryLib/Banner.html
Src/C_BoundaryLib/GNUmakefile

commit a903c3fdbaa5f1f6c4c1c0efad9e85c5695df190
Author: lijewski <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 9c9cc3f4cae1ebcf40cd2ce08a1512a7ffb2e14c
Author: lijewski <lijewski>
Date:   Wed May 6 17:50:30 1998 +0000

    Gunk for doing html and ps from Doc++ comments.

Src/C_AMRLib/Banner.html
Src/C_AMRLib/GNUmakefile

commit 4065246379ebbead96ac0930a683b28cfcddff4e
Author: car <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 2e849dd30ebb60f9eec3ccedf95cc50edb51297f
Author: car <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 36e345706b43d0d80eee1236eb3b5052c8748744
Author: lijewski <lijewski>
Date:   Mon May 4 23:13:13 1998 +0000

    Implemented ReduceBoolAnd() and ReduceBoolOr() for MPI.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 501687e6c569be69267e0c1147ee507526ef4b2f
Author: lijewski <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 3d75d1791fc253af1ce8335418c4b236459f2d07
Author: car <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 725ebfb1c1db546741aacba43b93ba5f375b7c91
Author: car <car>
Date:   Fri May 1 19:18:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_projector.cpp

commit d6af5171f4fc2700f4bda59bd14a5948e1de9768
Author: car <car>
Date:   Fri May 1 18:23:58 1998 +0000

    *** empty log message ***

Src/C_BaseLib/GNUmakefile
Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 82cfbb3faf9026d05f31dd4cd42417fc3cefdf4c
Author: lijewski <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 6f593dc5666a88e24c0783aa6e4ad71544bb8860
Author: lijewski <lijewski>
Date:   Thu Apr 30 18:04:33 1998 +0000

    Removed member template OpMin().

Src/C_BaseLib/Utility.H

commit 47d83a41751b99cbb214fc7551af82bc2f95b9f6
Author: lijewski <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 6cfe0d492fa84f34438274f3aebe564fd2ceb85f
Author: lijewski <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 994f11573bdcf568e0880f35303f2fcbea8eaed9
Author: lijewski <lijewski>
Date:   Wed Apr 29 23:12:37 1998 +0000

    fixed typo for GNUG workaround

Src/C_BaseLib/Geometry.H

commit 10c49047a59f44ddf4b2b4003cd0a821d5f87ab8
Author: car <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 4f2c5e7e8244fe9aa07bfade539d3bc41637bc5f
Author: lijewski <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 1e5580caa9084f08f3ee3c643c47a2b6bd25368d
Author: car <car>
Date:   Tue Apr 28 15:43:09 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 18becd91ca618f6fdf0fa530b05118f6fb746fd2
Author: car <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 6facb8f3ad66e230b1db90d97b567923bc023d38
Author: car <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 85457a0015bcd8874831f4b1b98320ec84d8763e
Author: lijewski <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 5c36262f7fce8561002659217a7232903c037425
Author: lijewski <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 c1b87b90e593c2544768e6a84f2a340479e22a72
Author: lijewski <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 5f0f443c491388c86caa476b0967694ce76c7d52
Author: car <car>
Date:   Mon Apr 27 17:37:40 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit feb36aedcfce10c9c217e0e1581183d00902b1c4
Author: car <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 3117be3c7078a956d406790498ef73d8b1ae9713
Author: lijewski <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 74c9a98670185ed2f8f56c46f1bae16b61b59367
Author: car <car>
Date:   Fri Apr 24 21:23:00 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 63316837b5f93d26e2db98edf4dd01185286c3d9
Author: car <car>
Date:   Fri Apr 24 21:19:47 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.cpp

commit 27a90a275414f655f6ded544b7dc29ea990063fc
Author: lijewski <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 d6c79da717ed38c092f58fba68f3ef33d272d3c3
Author: lijewski <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 54253935b5c4ee778db372d394e471f2be806e39
Author: lijewski <lijewski>
Date:   Fri Apr 24 16:28:57 1998 +0000

    Fixed typo.

Src/C_AMRLib/FluxRegister.cpp

commit 079352692c511336842938d7fe2a73f1c9d48ee3
Author: lijewski <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 36bb7bd43d760cb0e52c6ce5490b5b13a82b7e5b
Author: car <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 45011638c793f40ba1a1611093b3d4e9633e7c38
Author: lijewski <lijewski>
Date:   Fri Apr 24 00:11:38 1998 +0000

    Got CrseInit()/CrseInitFinish() working with MPI.

Src/C_AMRLib/FluxRegister.cpp

commit 63053cd1a62544c33c3c8ef71a31bfa6de12148d
Author: car <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 7304100f9614b89ab376d861daf51edf6849bc5b
Author: car <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 1eb2f400a98e15dc7809e2b636381676658b0540
Author: car <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 204cf3ddd7b9a7880a256f01aa6e7a44b2b2231a
Author: lijewski <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 a70d17694201c64df4dcf459587446be833ca59b
Author: car <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 59a97952804f8dd0b777767b3c07bc9291f9cab7
Author: car <car>
Date:   Thu Apr 23 04:48:44 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit d505119d824ea4e5e82630f06474e4d3e3827c17
Author: car <car>
Date:   Thu Apr 23 04:46:04 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real2d.F

commit 396fa27a89de8e666edf4a37e915c54f4e0671a9
Author: car <car>
Date:   Thu Apr 23 04:31:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit ee7d29c456c06d82ea2a7824c8646ac0b0fba3f6
Author: car <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 85f761238cad71087dfc1735a0d05c6a6ee40800
Author: almgren <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 b59392da518ec3f471d8d4af94cd8e07643440b9
Author: car <car>
Date:   Wed Apr 22 23:48:13 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_CellMG/LinOp.H

commit fac082321f94478e10ed08880bd00331296ddf0d
Author: marc <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 d7d03e61321535750297ed90e0c0cd27cdc608aa
Author: car <car>
Date:   Wed Apr 22 23:39:11 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/restrictor.cpp

commit 1e67c7076bf42af7b61af4105c6a16468de508d0
Author: car <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 b184bd934885569564f65f040d5a6768bf49b7af
Author: lijewski <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 59448e32c7730938bd22d8483c490204c597a497
Author: lijewski <lijewski>
Date:   Wed Apr 22 21:02:48 1998 +0000

    Wasn't erase()ing fabComTagList in MPI case.

Src/C_BaseLib/FabArray.H

commit 109dfddae71856ea891512c278e5906487301568
Author: car <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 45169e70271d7c38f7e02784881c95f78654e862
Author: lijewski <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 d475c6b66dc146fae3d5397c6059cbf15698ce7e
Author: lijewski <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 ee8a107cc852629b3a1260f17969d1860ae15097
Author: car <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 3c409a7c87275b0b3ace53558555635be2adf358
Author: almgren <almgren>
Date:   Tue Apr 21 22:22:41 1998 +0000

    Slight cleanup.

Src/LinearSolvers/C_NodalMG/proj.cpp

commit edc01757682052d39c38320033e671463d50e66e
Author: almgren <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 6c26d5dd8ecce000f1c9d3ac882af45fb581de23
Author: car <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 75b5b6073112c848756156c1785eff858bf6db4e
Author: marc <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 d520452f814de9c3034a7385976354b4e75160a4
Author: car <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 c735ed463ce53fe9be5a081b5f8adc2ac6b42317
Author: lijewski <lijewski>
Date:   Tue Apr 21 05:21:08 1998 +0000

    Made parallel-aware.

Src/C_BaseLib/Tracer.cpp

commit d57e0c1e60bffbc47eebf8513ff2535f2b9f6c55
Author: lijewski <lijewski>
Date:   Tue Apr 21 05:20:27 1998 +0000

    Commented out TRACER in StartParallel().

Src/C_BaseLib/ParallelDescriptor.cpp

commit e0625861331c0ee5efd1cbb2c9a53a8782a83cd7
Author: car <car>
Date:   Tue Apr 21 02:01:36 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 3c462c581ce1f9fdfbc13f03dda39e3dcbab6dd6
Author: marc <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 7bd9340f4e9f8d6c063b0b14bedb2ed5d30b3b18
Author: car <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 845495a0be5b93eafc274574e698f479bbf5dcb3
Author: car <car>
Date:   Mon Apr 20 22:57:07 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/interface.H

commit ea7c26ad081e872fbe127eb7a063048f3ca1a303
Author: lijewski <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 6370aca561925253107e6487bbff3c9570967513
Author: lijewski <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 d6e9549ee1d97dabc77a5c6da0f3868b84fe7ca6
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:18:29 1998 +0000

    Added TRACER objects to MPI calls.

Src/C_BaseLib/ParallelDescriptor.cpp

commit 2309e07bf1161cfb9afe0d4793630be3a253d579
Author: car <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 ca4ced5bd2ca432524d11258b12a7191b4530bd4
Author: lijewski <lijewski>
Date:   Mon Apr 20 22:16:38 1998 +0000

    Added fflush(stdout) after printf().

Src/C_BaseLib/Tracer.cpp

commit 98465ca1c0ab9328a7d9b2cbc2a792c10fbe3b63
Author: car <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 d67593938194375bde67bbac520dbb888c510c8a
Author: car <car>
Date:   Mon Apr 20 19:14:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/boundary.cpp

commit fe17ebe460f04f1c49c3004e9485812b2f1db6c5
Author: car <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 c94d744109f8d8cddc4a9281242b45ce38d1a1d7
Author: lijewski <lijewski>
Date:   Mon Apr 20 04:18:54 1998 +0000

    The sense of an Assert() was backwards.

Src/C_BaseLib/ParallelDescriptor.cpp

commit a332376b4886b038f29fdb87d81ceb964f25d639
Author: lijewski <lijewski>
Date:   Mon Apr 20 04:18:14 1998 +0000

    Fixed some MPI-specific bugs.

Src/C_BaseLib/VisMF.cpp

commit b21629ffdd60d5b4c084ca12f1b1f93ba67c7ece
Author: lijewski <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 c384ae692b80b26970506e695293d4e0684fe1a5
Author: lijewski <lijewski>
Date:   Sun Apr 19 03:46:05 1998 +0000

    MPI-specific code for FabArray::Copy(FAB).

Src/C_BaseLib/FabArray.H

commit 899a50cf4f6dcb018e19980b1c025dea86e2d3ba
Author: lijewski <lijewski>
Date:   Sat Apr 18 21:24:58 1998 +0000

    Added MPI-specific code for TagBoxArray::collate().

Src/C_AMRLib/TagBox.cpp

commit ee0e1e2c40f1f338f90c42c4b014e97d79615303
Author: car <car>
Date:   Fri Apr 17 23:25:08 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit b4301d3c7f381b43df39f2d3b6c4687a0c39c0db
Author: car <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 8da2bf87fa56c08a4ef775b81b0e062a35cdf89a
Author: lijewski <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 7fe0771fe1c9a71836e5a1cd4edac9efafdbcfd4
Author: lijewski <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 605051d8e388aeac8803d6cf098f7e2194f2137c
Author: car <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 98b6ea565333a32e32f83e9cf51bae36abc72973
Author: car <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 23db9b19cd634a9bdcffa28a6377956c291f9220
Author: lijewski <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 5cb1ad0b09f01fb47959384789d4fa61db708396
Author: lijewski <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 c8413243d4a265b6079812215bc155f04b9310fa
Author: car <car>
Date:   Fri Apr 17 16:40:11 1998 +0000

    check for non-existent test file

Src/LinearSolvers/C_NodalMG/proj.cpp

commit 3dc3a4f2c432e9afb27e3a380ba196a5f44c5678
Author: marc <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 a60bd99fa675483395f4f2111d01d29d1f2533c9
Author: car <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 27c25f320389c2ec41389a0b239acaf820985898
Author: lijewski <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 81d98d6a0bf2e798a567353b10f096c92c58a9a6
Author: car <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 738461f761efd138054697ede552546d3051482d
Author: lijewski <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 dbedfd15eec0db9ff118ccc2ef0fb9de1846c5b0
Author: lijewski <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 a1b52f9fc3536d8cb654a8a4f673f14c802491e5
Author: car <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 305938588e3ebf36fe0c5e02fe26ed9fbe50bc4e
Author: lijewski <lijewski>
Date:   Thu Apr 16 20:31:47 1998 +0000

    Fixed minor nit found by dbs.

Src/C_BaseLib/IntVect.cpp

commit 410c0c78db86ddfe8d589ebbc5dda54ad1f33131
Author: lijewski <lijewski>
Date:   Thu Apr 16 20:27:03 1998 +0000

    Some simplification in preparation for MPIification ...

Src/C_BaseLib/FabArray.H

commit 28965ddc033cd97d4d0b294816cfa214a291814f
Author: lijewski <lijewski>
Date:   Thu Apr 16 18:00:41 1998 +0000

    List<> -> vector<> ...

Src/C_BaseLib/FabArray.H

commit 44118e52e5a266d3a3543ba2bdae4d95436235a9
Author: car <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 0cc33d8c42736b2242b36682694f06ae3be672e5
Author: lijewski <lijewski>
Date:   Thu Apr 16 00:12:29 1998 +0000

    List<FillBoxId> -> vector<FillBoxId>.

Src/C_BoundaryLib/FabSet.cpp

commit 3e2db34f65fc7c4db12456707e4f3957882c60da
Author: marc <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 3a437bfd8b1c981c3dc6c7a3b013000f0096ab6a
Author: car <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 66e4dbf342615b7c135eeb894f68816154fbd8db
Author: lijewski <lijewski>
Date:   Wed Apr 15 23:31:28 1998 +0000

    List<> -> vector<> ...

Src/C_AMRLib/TagBox.cpp

commit e90d0210d6a545be9a1085389c0800b5d6c21fa1
Author: marc <marc>
Date:   Wed Apr 15 23:29:14 1998 +0000

    Oops! these were already in DataServices

Tools/C_util/README

commit 6d7a67405236448059d8e68b89f2b7e98dae52a4
Author: marc <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 cfecb97b2a206af7f93f2ba3f8bca7bcb59c3dca
Author: marc <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 a6e58bc1d9037574fe43cd52830956a969804762
Author: marc <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 8bed072465d592f19e49dacb0a0ceabc65459323
Author: lijewski <lijewski>
Date:   Wed Apr 15 22:49:54 1998 +0000

    List<FillBoxId> -> vector<FillBoxId>
    List<FabComTag> -> vector<FabComTag>.

Src/C_AMRLib/FluxRegister.cpp

commit e0ba06555178afb70df28208b280649956908751
Author: marc <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 c2c612f07b659317bb8f90cb912d65b798eda1f1
Author: marc <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 fe261f8f85593ad868cfcb82d217a114971170ac
Author: marc <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 cdea52552748b2672f813314d4e03c9c6c3158ac
Author: marc <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 470c9d1936a2f5b1f9c821c77c7b2bff3fc9c6cc
Author: marc <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 5bd08df7dda6bc1ae1bcf38e322fd26169231f6e
Author: marc <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 9d97b3659269fc0b29c4b079fee676c79f8dfec2
Author: lijewski <lijewski>
Date:   Wed Apr 15 21:18:31 1998 +0000

    Finished with MPI-specific code for now.

Src/C_AMRLib/FluxRegister.cpp

commit 83374ad9c5e044fbbb2a7c6f7b3f20b16f706411
Author: marc <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 276838b9eb669897208d79eae57c6b69af1104ba
Author: marc <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 3f1a9fbb910727576fe62def3492506621c86799
Author: lijewski <lijewski>
Date:   Wed Apr 15 18:04:11 1998 +0000

    More MPI-specific code.

Src/C_AMRLib/FluxRegister.cpp

commit 73af34280fa44f348ead07585326ef683eade25c
Author: lijewski <lijewski>
Date:   Wed Apr 15 16:50:45 1998 +0000

    Some MPIification ....  More to come.

Src/C_AMRLib/FluxRegister.cpp

commit 3e236e2080a28ecaab01a9c2fb58736ab52d19fa
Author: lijewski <lijewski>
Date:   Wed Apr 15 16:50:26 1998 +0000

    A tad bit of const'ification.

Src/C_AMRLib/TagBox.cpp

commit 5205caa48ee847824c3db58c53bec9c69c2476de
Author: lijewski <lijewski>
Date:   Tue Apr 14 23:57:43 1998 +0000

    Changed a few names to more mnemonic ones ...

Src/C_AMRLib/TagBox.cpp

commit f27c63174f54405e2e5f4a09943726497b42e81e
Author: lijewski <lijewski>
Date:   Tue Apr 14 23:01:50 1998 +0000

    Rearranged CrseInit() to facilitate MPI implementation.

Src/C_AMRLib/FluxRegister.cpp

commit 22b54ab9f8fd29e590d1418a583149f2140fb62e
Author: lijewski <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 e21fc3c2a428e8c5ba2895892556573c64861f6f
Author: lijewski <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 23fb2a6854a46ed10df7a0158ded29fa5bafe4db
Author: lijewski <lijewski>
Date:   Tue Apr 14 19:38:49 1998 +0000

    Optimized a few setVal() calls.

Src/C_BaseLib/FabArray.H

commit 64f0ccbcd3365da399009c5e5eb0c7dd9427ebfa
Author: car <car>
Date:   Tue Apr 14 17:30:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.cpp

commit a8122b0b5f21d5eba1503614f85899c4b208c61d
Author: car <car>
Date:   Tue Apr 14 17:07:24 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi.cpp

commit 2930465c7de5d633e88c2e81dab7654a3ce89012
Author: lijewski <lijewski>
Date:   Tue Apr 14 16:51:39 1998 +0000

    Added some (as yet untested) MPI-specific code.

Src/C_AMRLib/TagBox.cpp

commit f6b1c0a077d4e542841dcb6319df9ef8c953414b
Author: lijewski <lijewski>
Date:   Tue Apr 14 16:50:53 1998 +0000

    Fixed some syntax errors in MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 4987f80397ca23815d4e432fc0d5ca04cfccd790
Author: lijewski <lijewski>
Date:   Mon Apr 13 21:50:13 1998 +0000

    Some more (as yet untested) MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 517d20716c7230f29f3b8f0607b8d2c0bd1f10d9
Author: lijewski <lijewski>
Date:   Mon Apr 13 19:44:42 1998 +0000

    Added some (as yet) untested MPI-specific code.

Src/C_BaseLib/VisMF.cpp

commit 3c153e4425c6a0fb9192154e2349fae7ebfbe832
Author: lijewski <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 d1e7119e1b682c019e2314ebe6ff229ffbf885b2
Author: lijewski <lijewski>
Date:   Mon Apr 13 19:44:04 1998 +0000

    Added Abort(int) for MPI use.

Src/C_BaseLib/ParallelDescriptor.H

commit b2a703e18c47994adc48850e09601fe9dd332cee
Author: car <car>
Date:   Thu Apr 9 22:37:27 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 85c6f3514cadf0198fa0e28c0e2b553b88ded72b
Author: car <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 49aba79f5804c9f040204d1bfa7f26109fd2da7a
Author: car <car>
Date:   Thu Apr 9 16:18:10 1998 +0000

    added serial Gather

Src/C_BaseLib/ParallelDescriptor.cpp

commit bb74878615df02f0bef789096896ea4b4143d2eb
Author: lijewski <lijewski>
Date:   Wed Apr 8 23:42:52 1998 +0000

    Some more simplification.

Src/C_AMRLib/TagBox.cpp

commit 90034b2762c3f6721fb14b1995095170c847108e
Author: lijewski <lijewski>
Date:   Wed Apr 8 23:29:16 1998 +0000

    Some simplification.

Src/C_BaseLib/VisMF.cpp

commit c0cce08129441844e4899cbd62fc2bec46659492
Author: lijewski <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 d8efd9235a3fa469a26317eb41ff3952f6ed9fe2
Author: car <car>
Date:   Wed Apr 8 19:45:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit 03c24fcab890792b4ffa375d892106b0863e3cff
Author: car <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 a1cb2b93af61d55733668b0b348ce9f174e2f0f1
Author: lijewski <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 b1fe498fa99587db9f2d35f8628b9509896f7a1a
Author: lijewski <lijewski>
Date:   Tue Apr 7 22:24:44 1998 +0000

    More simplification.

Src/C_BaseLib/FabArray.H

commit af5b86effc4e36eb4e45cebede54a35fc1142727
Author: lijewski <lijewski>
Date:   Tue Apr 7 20:13:48 1998 +0000

    Simplified mergeUnique() a tad.

Src/C_AMRLib/TagBox.cpp

commit bf784f91509d66634b24344608e5fe46cc3aa3ae
Author: car <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 b8c55136a41fe773c3b2b6701806ac243cf8206c
Author: car <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 3a82fbb293b21aff8c70291c295887a14d29ce10
Author: car <car>
Date:   Tue Apr 7 17:36:02 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 7b6666c3b48b6587e937cfd0e06e8f0a5f31fc35
Author: car <car>
Date:   Tue Apr 7 17:24:21 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3.cpp

commit 604d85e7fdec50236ae7a1c51b3c8bfdf5764c34
Author: lijewski <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 eb3945456a8c11f1aafac650f60165020eb042a0
Author: car <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 4e8a4c256ebd8799b684d8b6dc3788bb735c0e3f
Author: lijewski <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 423664a90559e42a39bcf21afe127db8b965e872
Author: lijewski <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 da85cac2695c143bca21304b5ae5e8d888066070
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:22:27 1998 +0000

    Removed commented out Synchronize() calls.

Src/C_BaseLib/FabArray.H

commit f3bb677a5c1cf9d506ce3a8445b5f61c041c9aec
Author: lijewski <lijewski>
Date:   Wed Apr 1 18:21:50 1998 +0000

    Merged in Barrier().

Src/C_AMRLib/Amr.cpp
Src/C_AMRLib/AmrLevel.cpp

commit 683d22edce837a47230f1e8c4d57be941bab4fde
Author: lijewski <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 e550b5945589dac5ec2370871fe8e2bf5e2c2417
Author: car <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 9e402f58ab6949ea45c0d8d9058275845b9c93ba
Author: lijewski <lijewski>
Date:   Wed Apr 1 17:34:25 1998 +0000

    Added Banner.html for doc++ users.

Src/C_BaseLib/Banner.html

commit 34f21601c09afe51e276b7664f102aefa0b0620e
Author: car <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Sat Mar 28 00:45:04 1998 +0000

    NEWFPMINBOX -> BL_NEWFPMINBOX

Src/C_AMRLib/AmrLevel.cpp

commit 72302898b276f59704c360a816981d364651b4f7
Author: lijewski <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 <vince>
Date:   Fri Mar 27 18:34:00 1998 +0000

    Minor additions.

Tools/C_mk/Make.T3E

commit 8d2ee8f94a3e9b66b87f7e1f73c5f345107b19e7
Author: marc <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 <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 <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 <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 <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 <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 <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 <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 <almgren>
Date:   Thu Mar 26 17:51:58 1998 +0000

    Remove geom from setBndryConds call.

Src/C_BoundaryLib/InterpBndryData.cpp

commit 27aceb303de91d1d15f7416e9279ffc5a570dcc8
Author: almgren <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 <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 <lijewski>
Date:   Thu Mar 26 17:31:50 1998 +0000

    Uses new BoxArray::convert() function.

Src/C_AMRLib/AmrLevel.cpp

commit d60730e7b8a18b0a97f707f5e32862c1b36c044f
Author: lijewski <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 <car>
Date:   Wed Mar 25 20:59:54 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit fa287ca43aab056bfcdd5f8344a9a6438a603e1a
Author: car <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 <car>
Date:   Wed Mar 25 19:20:50 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit 69287608d46a6b3d28e275e048f17f5f4f060809
Author: car <car>
Date:   Wed Mar 25 19:17:47 1998 +0000

    *** empty log message ***

Src/C_BaseLib/ParallelDescriptor.cpp

commit b80eb3e3c7460bd9523c66a7c247744c5a41645f
Author: car <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Mon Mar 23 21:03:17 1998 +0000

    Now maintain DeriveRec in List<DeriveRec> instead of List<DeriveRec*>

Src/C_AMRLib/Derive.H
Src/C_AMRLib/Derive.cpp

commit 9de50888e7e7ea480229214ec169ac4393f3402f
Author: lijewski <lijewski>
Date:   Mon Mar 23 21:02:56 1998 +0000

    Now maintain ErrorRec in List<ErrorRec> not List<ErrorRec*>

Src/C_AMRLib/ErrorList.H
Src/C_AMRLib/ErrorList.cpp

commit b823cc551e8037d7eaf09d78517ced580412f9aa
Author: lijewski <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 <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 <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 <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 <car>
Date:   Sun Mar 15 23:44:53 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 061a52241c3255ff6eb4f32993b8c31afd4822f5
Author: car <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <car>
Date:   Sun Mar 1 22:17:46 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 53a1e97f0def542902a922f992aaf076e1dadfee
Author: car <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 <car>
Date:   Sun Mar 1 21:51:51 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 6a52dfb6666a010b61c2873c79f5341c1a7e02d1
Author: car <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 <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 <car>
Date:   Fri Feb 27 21:03:44 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 0398cf30094464180464c32a7b1dcbf5f43af0ef
Author: car <car>
Date:   Fri Feb 27 21:01:17 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit a0565f3f87cbee8af57f78825fb2a549aac6d0f8
Author: car <car>
Date:   Fri Feb 27 20:59:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit d7ab03739737010b94d4fb22d180406feef80901
Author: lijewski <lijewski>
Date:   Thu Feb 26 22:07:57 1998 +0000

    Made isStateVariable() static.

Src/C_AMRLib/AmrLevel.H

commit c38372b5d6f5474df5301bf23164cb6b000c7483
Author: car <car>
Date:   Wed Feb 25 23:24:16 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit 72ed30f6a11b06e4439257dc08e70818243a49cd
Author: car <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 <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 <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 <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 <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 <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 <car>
Date:   Sun Feb 22 19:24:25 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 0e2eebe0744aabdf9613bf9b89865de8d4b7fc1b
Author: car <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 <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 <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 <car>
Date:   Sun Feb 22 01:36:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit c7c57052a1d62e6ced9fe59c09b0a73930b28f4e
Author: car <car>
Date:   Sun Feb 22 01:35:39 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit eb32a57e2feb407515678c1b7cf1a3fc18ebb53b
Author: car <car>
Date:   Sun Feb 22 01:32:20 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 0a51bb21226c81586d647f8b8ad9e3b952575c20
Author: car <car>
Date:   Sun Feb 22 01:30:02 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 7c77304daba83b6ca60b4f868570c08232e6b1c5
Author: car <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 <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 <car>
Date:   Fri Feb 20 21:49:27 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit d3bcb9cab2afcdf74b7dd8ee98b52b5f8cf0161d
Author: car <car>
Date:   Fri Feb 20 21:46:52 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit c769567ce01d62880f0dfd8d32514802c5a9f0b6
Author: car <car>
Date:   Fri Feb 20 21:42:58 1998 +0000

    *** empty log message ***

Src/LinearSolvers/C_NodalMG/hg_proj3d.F

commit e40ee2c7831c132431b95f1aa3205ed59b89407b
Author: car <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 <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 <vince>
Date:   Fri Feb 20 18:30:47 1998 +0000

    Optimized FillFab and fabCopyDescList.

Src/C_BaseLib/FabArray.H

commit 25c020128bd956dcf07eb6c1f0e78b9b162357ad
Author: car <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 <lijewski>
Date:   Thu Feb 19 18:10:46 1998 +0000

    Added default constructor to TagBoxMergeDesc.

Src/C_AMRLib/TagBox.cpp

commit 64833abe26920c9f796f1660f983b28f285b216f
Author: lijewski <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 <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 <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 <vince>
Date:   Wed Feb 18 21:38:11 1998 +0000

    Removed fortran apprentice flag.

Tools/C_mk/Make.T3E

commit 03bbc3c5d1060720fcdd181c664a1f88d0ae8ef0
Author: vince <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 <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 <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 <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 <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 <lijewski>
Date:   Tue Feb 17 22:42:04 1998 +0000

    Added a RunStats variable for parallel sync time.
    No longer need to include <Utility.H> in <ParallelDescritor.H>.

Src/C_BaseLib/ParallelDescriptor.H
Src/C_BaseLib/ParallelDescriptor.cpp

commit 6255667f18e56878cc262b6f42e82a773605afd4
Author: car <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 <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 <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 <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 <vince>
Date:   Thu Feb 12 22:16:24 1998 +0000

    Initialized m_pa.

Src/C_BaseLib/VisMF.cpp

commit 00571d09626ce3a98a5fe324d94dc3d521851f47
Author: lijewski <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 <car>
Date:   Thu Feb 12 17:32:10 1998 +0000

    win32 changes

Src/C_BaseLib/Utility.cpp

commit c36759a831238ee7427d7d62b1b0c7a9a4d0db9c
Author: lijewski <lijewski>
Date:   Thu Feb 12 16:56:08 1998 +0000

    Fixed bug in getline().

Src/C_BaseLib/aString.cpp

commit e304a4e09dbd0a086ffcf5f1f8d967f6b62ec1d3
Author: car <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 <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 <lijewski>
Date:   Mon Feb 9 22:45:58 1998 +0000

    Mods for T3E and g++.

Src/C_BaseLib/CArena.cpp

commit 15611985d70f567879568b465b10497ee49fdfd2
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <car>
Date:   Fri Feb 6 16:53:10 1998 +0000

    Array bust

Src/LinearSolvers/C_NodalMG/amr_real3d.F

commit ea263bbdb882b15f46b627d76dd003cf75db315e
Author: vince <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 <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 <vince>
Date:   Thu Feb 5 22:15:55 1998 +0000

    Fixed a typo.

Src/C_BaseLib/COORDSYS_3D.F

commit ce8e8875aaa54119fc5223e0300bc22a452e5295
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Thu Jan 29 18:59:36 1998 +0000

    Lowered the size of ChunkSize.

Src/C_AMRLib/TagBox.H

commit 9ea937d02230e09230daea9ecc46f9a8f94fd56d
Author: car <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Mon Jan 26 23:16:20 1998 +0000

    Removed unused function.

Src/C_AMRLib/Cluster.H

commit 1283da021cd32ef3581fcd626b6c4f0eff7b6832
Author: lijewski <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 <lijewski>
Date:   Mon Jan 26 21:57:18 1998 +0000

    We're now derived from BaseFab<char>
    Added tags() and tags(Array<int>) to support Fortran.

Src/C_AMRLib/TagBox.H
Src/C_AMRLib/TagBox.cpp

commit 92cfb5d77a6ce97826b8a16ccba328c747852823
Author: car <car>
Date:   Mon Jan 26 20:56:19 1998 +0000

    Fixes.

Src/LinearSolvers/C_NodalMG/GNUmakefile.main

commit 0c8d38d2efd648d98d406865f649ac5809efeb09
Author: car <car>
Date:   Mon Jan 26 20:20:55 1998 +0000

    for loop index

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit 3f9d86f2c7ef25aa91fb662bed03e15ee7c05105
Author: car <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 <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 <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 <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 <lijewski>
Date:   Fri Jan 23 17:51:31 1998 +0000

    Reduced memory usage in colate().

Src/C_AMRLib/TagBox.cpp

commit f2e77a3fe0028db1bb5e80d8395894e7bdaa1c8f
Author: car <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 <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 <car>
Date:   Wed Jan 21 22:57:52 1998 +0000

    Caching removed.

Src/LinearSolvers/C_NodalMG/hgproj.dsp

commit 3a6802b773dc2e15ed9e50def231b79dc077d623
Author: car <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 <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 <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 <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 <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 <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 <vince>
Date:   Wed Jan 21 19:32:12 1998 +0000

    Minor change for the cray.

Src/C_AMRLib/DatasetClient.cpp

commit cb75afca46ce7b18430e6d9f2813854612a297e8
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <car>
Date:   Tue Dec 23 05:15:52 1997 +0000

    Fix for win32.

Src/C_BoundaryLib/bndrylib.dsp

commit 9473074d92c11a725ce89060e0726e3cfc07441d
Author: car <car>
Date:   Tue Dec 23 05:15:15 1997 +0000

    Change for Win32.

Src/C_AMRLib/amrlib.dsp

commit 1249c6591b446e9c0902092644a64d75d90ee257
Author: car <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 <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 <lijewski>
Date:   Fri Dec 19 21:54:45 1997 +0000

    Removed List<T>::copy().  Just a memory leak waiting to happen.

Src/C_BaseLib/List.H

commit 681924cacad520171cc2d8f8f88d0808a19ebb7f
Author: lijewski <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 <lijewski>
Date:   Fri Dec 19 18:43:51 1997 +0000

    getBCArray() now returns Array<int> not int*.

Src/C_AMRLib/AmrLevel.H
Src/C_AMRLib/AmrLevel.cpp

commit fcf695131501679e53d72e44cb0fde25017848c1
Author: lijewski <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 <lijewski>
Date:   Wed Dec 17 23:04:53 1997 +0000

    Now need <Utility.H>

Src/C_AMRLib/AmrLevel.cpp

commit f352fec4d8eb703e3e1b3afbd6a043a3dc931ccd
Author: lijewski <lijewski>
Date:   Wed Dec 17 23:04:32 1997 +0000

    Removed need for <Utility.H>

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 <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 <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 <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 <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 <car>
Date:   Tue Dec 16 15:27:47 1997 +0000

    Make a warning go away.

Src/C_BaseLib/RunStats.cpp

commit fa0ef937808dc73214eb9a10f457dd217bdb8358
Author: lijewski <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 <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 <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 <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 <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 <car>
Date:   Sat Dec 13 21:09:28 1997 +0000

    Compile rule changes.

Src/C_AMRLib/amrlib.dsp

commit 0a499e0803a493c0ca5adddc4eb347505878e82d
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Thu Dec 11 06:14:02 1997 +0000

    A few more endls added.

Src/C_AMRLib/Amr.cpp

commit 611e3a3d57d80e13fc2f0708c1514d790d26b911
Author: lijewski <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 <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 <lijewski>
Date:   Wed Dec 10 22:04:42 1997 +0000

    Added DIMS==1 stuff.

Src/C_AMRLib/DIMS.H

commit 941c34764fdce5a833861ed1591a436c1ec63709
Author: lijewski <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 <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 <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 <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 <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 <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<FArrayBox*>* 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 <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 <lijewski>
Date:   Fri Dec 5 22:07:31 1997 +0000

    Some consolidation.

Tools/C_mk/Make.T3E

commit 73822ae6714999728658448baccaf85b36fb90b4
Author: car <car>
Date:   Fri Dec 5 19:07:30 1997 +0000

    Give an argument to ::time()

Src/C_BaseLib/Utility.cpp

commit 041888b9739ec659c8e5a6cf0a69146730f0a9bb
Author: lijewski <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 <lijewski>
Date:   Fri Dec 5 16:18:22 1997 +0000

    Added clear() and clear(int).

Src/C_BaseLib/VisMF.H

commit d814232dc3a7f7da34ce84fb069cfb1e9e990f94
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Wed Dec 3 03:26:57 1997 +0000

    Performance modification to performSetVal().

Src/C_BaseLib/BaseFab.H

commit b9d9755a1441e78a36b7d7252e284ac3d7fcaede
Author: lijewski <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 <lijewski>
Date:   Tue Dec 2 23:40:32 1997 +0000

    Merged with one from IAMRAll.

Src/C_AMRLib/FluxRegister.cpp

commit dcaba019a2fd0d31427420f46d3336a3a1e3d933
Author: lijewski <lijewski>
Date:   Tue Dec 2 23:05:28 1997 +0000

    Merged with IAMRAll.

Src/C_AMRLib/TagBox.cpp

commit 3cc8b18f0d6eb3ed26891ea45ec2f832e6fcbf28
Author: lijewski <lijewski>
Date:   Tue Dec 2 21:30:56 1997 +0000

    Updated from IAMRAll.

Src/C_AMRLib/StateData.cpp

commit a211f6340f445ba6a77b020c09761aaa8717764a
Author: lijewski <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 <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 <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 <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 <vince>
Date:   Mon Dec 1 20:49:58 1997 +0000

    Added ifdefs for the T3E.

Src/C_BaseLib/CONSTANTS.H

commit bdbd2a0966e7027277119d5c831377780c7add9a
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <car>
Date:   Tue Nov 25 19:55:15 1997 +0000

    Assertion for nprocessors > 1

Src/C_BaseLib/DistributionMapping.cpp

commit e343caa0f06827f5ad07b57e1aed6a9c06be2f14
Author: lijewski <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 <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 <car>
Date:   Tue Nov 25 19:00:36 1997 +0000

    Improvements in DistributionMapping for Knapsack

Src/C_BaseLib/DistributionMapping.cpp

commit dbaffef3482714b2aa5279b0eccfb7fc6c22d7fa
Author: lijewski <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 <lijewski>
Date:   Tue Nov 25 17:08:25 1997 +0000

    Small changes ...

Src/C_BaseLib/DistributionMapping.cpp

commit 68fa915dfbc2338a1e6c57fa9a09c358d55e8db2
Author: car <car>
Date:   Tue Nov 25 14:49:30 1997 +0000

    Removed use of member template.

Src/C_BaseLib/DistributionMapping.cpp

commit 07c667a8064c45af21efc3b105b3c94482d8cb13
Author: lijewski <lijewski>
Date:   Mon Nov 24 23:45:51 1997 +0000

    Added initializer for wsecond().

Src/C_BaseLib/Utility.cpp

commit d713dc76066ff10d8180db70214104cb995a8a03
Author: car <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 <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 <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 <lijewski>
Date:   Mon Nov 24 18:40:53 1997 +0000

    Minor mod to output formatting.

Src/C_AMRLib/RunStats.cpp

commit 2d82e5ad5a4d6db9004cf9cff738e996bba85906
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Thu Nov 20 16:13:38 1997 +0000

    A small simplification.

Src/C_BaseLib/ParallelDescriptor.H

commit 3b1715cd2d8567bb8161758b1dcf21e051413a2a
Author: lijewski <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 <lijewski>
Date:   Thu Nov 20 00:19:50 1997 +0000

    Added PrintStats() to FabArray.

Src/C_BaseLib/FabArray.H

commit 69d07d5b9af87d1a4313555ae1b6f5d918958d4d
Author: lijewski <lijewski>
Date:   Thu Nov 20 00:19:30 1997 +0000

    Prettified report() a tad.

Src/C_AMRLib/RunStats.cpp

commit 235c008475187c04dd7ae36eb8f520deded123b9
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <vince>
Date:   Fri Nov 14 21:43:35 1997 +0000

    Added better optimization flags.

Tools/C_mk/Make.T3E

commit 42f1aeaee1b13f53c6dba9329afa8d4224b6b43e
Author: lijewski <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 <lijewski>
Date:   Fri Nov 14 00:59:55 1997 +0000

    Removed Large_IO_Buffer() and replaced with Array<Setbuf_Char_type> usage.

Src/C_BaseLib/VisMF.H
Src/C_BaseLib/VisMF.cpp

commit 93d90f6eb05e1fd98ebda7e80c851c0348d47b54
Author: lijewski <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 <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 <lijewski>
Date:   Thu Nov 13 21:41:23 1997 +0000

    Added BL_USE_SETBUF.

Tools/C_mk/Make.T3E

commit 8bf2453b733cc05f0dc021a7de03d5e2c32e9813
Author: lijewski <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 <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 <lijewski>
Date:   Thu Nov 13 16:38:54 1997 +0000

    Replaced abort() with BoxLib::Abort().

Src/C_BaseLib/ParallelDescriptor.H

commit 6f6535f7e59c6cb39deb231ee6499dfeec634d69
Author: lijewski <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 <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 <vince>
Date:   Thu Nov 13 01:14:43 1997 +0000

    Make definitions for the T3E.

Tools/C_mk/Make.T3E

commit 34c3ce53861205acf3f172113da3aed1cd192bcf
Author: lijewski <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 <nazgul>
Date:   Wed Nov 12 22:10:30 1997 +0000

    fiddling with test problems

Src/LinearSolvers/C_NodalMG/proj.cpp

commit ea17c0a6c99aacaa2f5f90d2ac06e4c7ddbd54bd
Author: lijewski <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 <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 <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 <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 <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 <lijewski>
Date:   Wed Nov 12 00:22:57 1997 +0000

    Added .cvsignore

Src/C_BaseLib/.cvsignore

commit 7b0886b7799558836552352318143a04261bea94
Author: lijewski <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 <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 <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 <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 <vince>
Date:   Tue Nov 11 21:04:52 1997 +0000

    Added sync argument:  FabArrayIterator<T>::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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <jbb>
Date:   Sat Nov 8 01:42:02 1997 +0000

    Fixed nested comments

Src/C_BaseLib/Utility.H

commit 9e289e25a32fda9c0bf218d99f2b66a2320861ae
Author: almgren <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 <almgren>
Date:   Thu Oct 30 22:44:13 1997 +0000

    Cosmetic changes only.

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 6cd1d16687afdf6e5465cc44323f4c35c4d37cde
Author: vince <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 <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 <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 <car>
Date:   Thu Sep 25 21:57:17 1997 +0000

    Small changes.

Src/C_BaseLib/pBoxLib_2.dsp

commit 949841b53c75d1a257cc5db73618a1155deb50c9
Author: lijewski <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 <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 <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 <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 <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 <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 <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 <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 <car>
Date:   Fri Sep 19 16:17:30 1997 +0000

    Change Comment.

Src/C_BaseLib/ArrayLim.H

commit 111550f24a68ea03c41d1098dd55de0b050e3340
Author: lijewski <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 <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 <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 <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 <car>
Date:   Thu Sep 18 18:25:19 1997 +0000

    Added some stuff.

Src/C_BaseLib/pBoxLib_2.dsp

commit 2dd0ee07696f36f5b6bf3400857e317ebfcefd6a
Author: car <car>
Date:   Thu Sep 18 18:18:01 1997 +0000

    Broke a comment.

Src/C_BaseLib/Utility.H

commit cb25311b3520630c59588f83a55157e4913dd78e
Author: car <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 <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 <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 <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Tue Sep 16 21:11:34 1997 +0000

    Removed all virtual stuff.

Src/C_BaseLib/FabArray.H

commit 980dde8029d140ae76d2d05700648d63159e2d93
Author: lijewski <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 <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 <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 <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 <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 <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 <lijewski>
Date:   Mon Sep 15 20:46:01 1997 +0000

    Now assume things at ../mk

Tools/C_mk/Make.defs

commit 296a7d000fe41bc59e4b42fa1f3ba2b2a5ec2196
Author: lijewski <lijewski>
Date:   Mon Sep 15 20:45:43 1997 +0000

    Now assume ../mk existance.

Src/C_BaseLib/GNUmakefile

commit 1c282a382a7493b9332146ca3a08220cb1374021
Author: lijewski <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 <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 <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 <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 <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 <car>
Date:   Mon Aug 11 23:45:38 1997 +0000

    Fortran tweaks.

Src/C_AMRLib/DatasetClient.cpp

commit dd6443e646e9f29410d9c7ff897a43bbbc280159
Author: nazgul <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 <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 <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 <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 <vince>
Date:   Thu Jul 24 20:31:14 1997 +0000

    Added more FillPatchIterators.

Src/C_AMRLib/DatasetClient.cpp

commit 3976a1d77302700e9b5717fe6712f60c2578f5ea
Author: nazgul <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <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 <nazgul>
Date:   Thu May 8 15:18:17 1997 +0000

    Removed the function type(const PArray<MultiFab>& a).
    It was too prone to errors caused by partially-filled arrays.
    Use type(const FabArray<Real,Fab>& 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 <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 <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 <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 <nazgul>
Date:   Wed May 7 01:37:55 1997 +0000

    adding line solve

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 5bca72009eeb1c3d2f869563ae4261a411f18a97
Author: nazgul <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 <nazgul>
Date:   Tue May 6 03:11:18 1997 +0000

    fix index bug

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit bad568c5614578c49cbee45558f823110a6ab6e9
Author: nazgul <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 <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 <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 <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 <nazgul>
Date:   Wed Apr 30 20:28:51 1997 +0000

    adding GNUmakefile manually since import ignores it.

Src/LinearSolvers/C_NodalMG/GNUmakefile

commit 67746f0dc469437c4a66c7c74e478ac6223deef4
Author: nazgul <nazgul>
Date:   Wed Apr 30 20:03:52 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_defs.H

commit 912dae00eccf22fa9f468469c07b3e03884eca74
Author: nazgul <nazgul>
Date:   Wed Apr 30 19:40:01 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_graph.H
Src/LinearSolvers/C_NodalMG/amr_graph.cpp

commit 2593ad549b300c9030f9c96f2b92da94a607a040
Author: nazgul <nazgul>
Date:   Wed Apr 30 17:35:40 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi2.cpp

commit eb88f1d8f9edbec08451464a1a58adc58c9a315c
Author: nazgul <nazgul>
Date:   Wed Apr 30 17:26:18 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_multi.cpp

commit a153bb642f43c1f0dc43e9dda19224ca33bf0abd
Author: nazgul <nazgul>
Date:   Tue Apr 29 22:40:14 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/boundary.cpp
Src/LinearSolvers/C_NodalMG/interface.cpp

commit fa663bf79c0f70141d03350f32c0ebf913e88c08
Author: nazgul <nazgul>
Date:   Tue Apr 29 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 <nazgul>
Date:   Tue Apr 29 20:38:16 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/fill_patch.H

commit 5e43618b9ba22ff0405611be875aed141fb2971a
Author: nazgul <nazgul>
Date:   Tue Apr 29 20:15:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi1.cpp

commit ba18f4dd9f6dfa86e00df173cf66154acc1ead2e
Author: nazgul <nazgul>
Date:   Tue Apr 29 18:29:40 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi2d.F

commit 94ffd818a9bf1ab6c86ec18e6e4565395f40ff4e
Author: nazgul <nazgul>
Date:   Mon Apr 28 21:51:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_multi.H

commit a498100b0a43479409605ec9eaa464600fe1621b
Author: nazgul <nazgul>
Date:   Fri Apr 25 23:30:33 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/Make.package

commit 0f2561a87bce705882fc6124212c47013f79abea
Author: nazgul <nazgul>
Date:   Wed Apr 23 22:34:37 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/GNUmakefile.main

commit f686b4bc929214d97a8b0588608fe3b6731e46dc
Author: nazgul <nazgul>
Date:   Thu Mar 27 22:05:28 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi.H

commit 52d19b7261ae7399004472ae95a884a86413590c
Author: nazgul <nazgul>
Date:   Thu Mar 27 21:24:11 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_projector.H

commit 6b3d4c19412bdbce7f963ddded8121c512d600c1
Author: nazgul <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 <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 <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 <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 <nazgul>
Date:   Thu Mar 20 21:13:29 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/Rewrite

commit 2e93f82c5955ee9919b5c73c2a318745843ac9f0
Author: nazgul <nazgul>
Date:   Tue Mar 18 23:51:41 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/cache.H

commit 003ce6b53e5b81ecd219bc5a44af8d244e71f26a
Author: nazgul <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
Author: nazgul <nazgul>
Date:   Tue Mar 11 21:41:59 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_avg2d.F
Src/LinearSolvers/C_NodalMG/hg_avg3d.F

commit 3c64577c7f70412dbff59ecc2e3f6e3af9daeb27
Author: nazgul <nazgul>
Date:   Mon Mar 3 18:05:45 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gtjbb2
Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb2

commit 0e784304318d972a12ff33b3ea641a81a402e790
Author: nazgul <nazgul>
Date:   Thu Feb 27 22:39:56 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/restrictor.H

commit 20def58b10e8becad27f7bff656cd10695829880
Author: nazgul <nazgul>
Date:   Wed Feb 26 20:41:58 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/interpolator.H
Src/LinearSolvers/C_NodalMG/interpolator.cpp

commit e2cac3e6437f670bdb29e607b8f777d3c23c1dd5
Author: nazgul <nazgul>
Date:   Tue Jan 28 18:30:30 1997 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr.19l3
Src/LinearSolvers/C_NodalMG/tests/gr3ann
Src/LinearSolvers/C_NodalMG/tests/gr3ann2
Src/LinearSolvers/C_NodalMG/tests/gtrick
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19l3
Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann
Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann2
Tests/LinearSolvers/C_NodalMG/test_grids/gtrick

commit ee9a62eadae53a655b766d757aaeb56b5ff725a3
Author: nazgul <nazgul>
Date:   Tue Sep 24 19:39:37 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/mall_info.cpp

commit 928a1d7dde9f59786478d389194e2a0d314e6c8b
Author: nazgul <nazgul>
Date:   Sat Aug 31 00:51:34 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_multi3d.F

commit 3931ee9d0cc9f7a1baeba373b1a4fa2dc915f118
Author: nazgul <nazgul>
Date:   Tue May 14 20:11:34 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/tests/gr.19s8
Src/LinearSolvers/C_NodalMG/tests/gr2a8
Src/LinearSolvers/C_NodalMG/tests/gr3rick
Src/LinearSolvers/C_NodalMG/tests/gr3rick2
Src/LinearSolvers/C_NodalMG/tests/gt3ann
Src/LinearSolvers/C_NodalMG/tests/gtjbb
Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s8
Tests/LinearSolvers/C_NodalMG/test_grids/gr2a8
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 <nazgul>
Date:   Thu Apr 25 16:46:17 1996 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_proj2d.F

commit 1f04efac2dc02158cf22a7c3d2f3f87082487dc6
Author: nazgul <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 <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 <nazgul>
Date:   Mon Oct 30 22:35:09 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/README

commit cfefdf25849ecf2ab5a5b2b6573a4f2bc43a21dd
Author: nazgul <nazgul>
Date:   Mon Sep 18 20:37:46 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/poisson.cpp

commit d3a6d7bfeffcf89aa95b004c4aabb44f9243f13c
Author: nazgul <nazgul>
Date:   Mon Sep 18 18:20:14 1995 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp

commit e7ab65e98df0bd6814dab6ea6bb540296b1b4677
Author: nazgul <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 <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 <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 <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
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p3
Src/LinearSolvers/C_NodalMG/tests/gr2ann.p4
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/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/gr3.rz
Src/LinearSolvers/C_NodalMG/tests/gr3a
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/gr4
Src/LinearSolvers/C_NodalMG/tests/gt.32
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
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/gtgrav2
Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav4
Tests/LinearSolvers/C_NodalMG/test_grids/gtpfail

commit d9792e7e53274b898d907a0f08452bef75669031
Author: nazgul <nazgul>
Date:   Tue Oct 4 22:13:47 1994 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/amr_gravity.H

commit b06aef4481e3612148772e1a6e0aa59c3be684e4
Author: nazgul <nazgul>
Date:   Wed Mar 23 23:31:05 1994 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/hg_elliptic.H

commit 1fc596b76899cdd13da6cd2998ba4f362c5b3130
Author: nazgul <nazgul>
Date:   Tue Oct 5 18:46:17 1993 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/driver.cpp

commit 93dbd8bb612ee031f19d5659b3b8aac4afb85511
Author: nazgul <nazgul>
Date:   Fri Mar 12 19:37:55 1993 +0000

    Initial revision

Src/LinearSolvers/C_NodalMG/RegType.H